RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2786
(198 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 = 50.3 bits (121), Expect = 2e-08
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 10/79 (12%)
Query: 3 YAVKIAS-CPANPTYSLLFPDN---IDADIYPPNKPKPLCLRVH-----LLCYGKQLAFL 53
A+++A +F D+ + A + P PL LR+ L +G ++
Sbjct: 47 EALQLALREGRRARKITIFSDSQAALKA-LRSPRSSSPLVLRIRKAIRELANHGVKVRLH 105
Query: 54 WCPSHTGIQGNEAVDRAAR 72
W P H+GI+GNE DR A+
Sbjct: 106 WVPGHSGIEGNERADRLAK 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 = 41.9 bits (99), Expect = 3e-05
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 32 NKPKPLCLRVH-LLCYGKQLAFLWCPSHTGIQGNEAVDRAAR 72
++ KP+ + LL ++ W P H+GI GNE D+ A+
Sbjct: 81 SESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAK 122
>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 = 35.9 bits (84), Expect = 0.004
Identities = 10/29 (34%), Positives = 12/29 (41%)
Query: 44 LCYGKQLAFLWCPSHTGIQGNEAVDRAAR 72
L Q+ + W H G GNE D A
Sbjct: 107 LLAKHQVTWHWVKGHAGHPGNERADELAN 135
>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 = 32.9 bits (76), Expect = 0.044
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 52 FLWCPSHTGIQGNEAVDRAARN 73
F+ +H+G + NE D+ A+
Sbjct: 110 FVKVKAHSGDKYNELADKLAKK 131
>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 = 31.9 bits (73), Expect = 0.077
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 48 KQLAFLWCPSHTG-----IQGNEAVDRAAR 72
K +A + +H+G GN D+AAR
Sbjct: 103 KPVAVIHIRAHSGLPGPLALGNARADQAAR 132
>gnl|CDD|188606 TIGR04091, LTA_dltB, D-alanyl-lipoteichoic acid biosynthesis
protein DltB. Members of this protein family are DltB,
part of a four-gene operon for D-alanyl-lipoteichoic
acid biosynthesis that is present in the vast majority
of low-GC Gram-positive organisms. This protein may be
involved in transport of D-alanine across the plasma
membrane [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 380
Score = 31.4 bits (72), Expect = 0.30
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 85 SPEDF-KPFIHKLIKDLWQNSW 105
+P +F KPF+ K IKD W N W
Sbjct: 250 TPMNFNKPFLSKDIKDFW-NRW 270
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 29.6 bits (67), Expect = 0.53
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 54 WCPSHTGIQGNEAVDRAAR 72
W H G NE D+ AR
Sbjct: 122 WVKGHAGHPENERADQLAR 140
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.4 bits (66), Expect = 1.0
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 93 IHKLIKDLWQNSWSNI-----PNCNK---LKSIKPVIGPWPSSDRQNRHEEVVI 138
+ LIKDL+QN W N P K L+ I ++ Q ++V I
Sbjct: 125 ANPLIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLS---DGINQFLPKKVGI 175
>gnl|CDD|238366 cd00714, GFAT, Glutamine amidotransferases class-II
(Gn-AT)_GFAT-type. This domain is found at the
N-terminus of glucosamine-6P synthase (GlmS, or GFAT in
humans). The glutaminase domain catalyzes amide
nitrogen transfer from glutamine to the appropriate
substrate. In this process, glutamine is hydrolyzed to
glutamic acid and ammonia. In humans, GFAT catalyzes the
first and rate-limiting step of hexosamine metabolism,
the conversion of D-fructose-6P (Fru6P) into
D-glucosamine-6P using L-glutamine as a nitrogen source.
The end product of this pathway, UDP-N-acetyl
glucosamine, is a major building block of the bacterial
peptidoglycan and fungal chitin.
Length = 215
Score = 28.6 bits (65), Expect = 1.8
Identities = 9/10 (90%), Positives = 9/10 (90%), Gaps = 1/10 (10%)
Query: 143 IGHTR-ATHG 151
IGHTR ATHG
Sbjct: 68 IGHTRWATHG 77
>gnl|CDD|152066 pfam11630, DUF3254, Protein of unknown function (DUF3254). This
family of proteins is most likely a family of
anti-lipopolysaccharide factor proteins however this
cannot be confirmed.
Length = 97
Score = 27.3 bits (61), Expect = 2.4
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 7/48 (14%)
Query: 53 LWCPSHTGIQGN-------EAVDRAARNPSASLPPLKLCSPEDFKPFI 93
+WCP T I G V+ A R+ L + E+ ++
Sbjct: 49 MWCPGWTPITGESRTRSRSGVVEHAVRDFVQKALQAGLITEEEANAWL 96
>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 = 2.6
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 47 GKQLAFLWCPSHTGIQGNEAVDRAAR 72
G ++ F P H+GI GNE DR A+
Sbjct: 121 GIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|223526 COG0449, GlmS, Glucosamine 6-phosphate synthetase, contains
amidotransferase and phosphosugar isomerase domains
[Cell envelope biogenesis, outer membrane].
Length = 597
Score = 28.3 bits (64), Expect = 2.9
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 134 EEVVICRMRIGHTR-ATHG 151
+E +I + I HTR ATHG
Sbjct: 61 KEPLIGGVGIAHTRWATHG 79
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 27.1 bits (60), Expect = 4.4
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 57 SHTGIQGNEAVDRAA 71
+H+GI+GNEA D A
Sbjct: 127 AHSGIEGNEAADMLA 141
>gnl|CDD|183716 PRK12744, PRK12744, short chain dehydrogenase; Provisional.
Length = 257
Score = 27.4 bits (61), Expect = 5.3
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 4/43 (9%)
Query: 63 GNEAVDRAARNPSAS----LPPLKLCSPEDFKPFIHKLIKDLW 101
E + A + +A+ L ED PFI L+ D W
Sbjct: 199 PQEGAEAVAYHKTAAALSPFSKTGLTDIEDIVPFIRFLVTDGW 241
>gnl|CDD|151789 pfam11348, DUF3150, Protein of unknown function (DUF3150). This
bacterial family of proteins with unknown function
appears to be restricted to Proteobacteria.
Length = 257
Score = 27.2 bits (61), Expect = 5.9
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 76 ASLPPLKLCSPEDFKPFIHKL 96
ASL K+ PE KPF KL
Sbjct: 38 ASLGSKKIIDPEALKPF-SKL 57
>gnl|CDD|177613 PHA03376, PHA03376, BARF1; Provisional.
Length = 221
Score = 27.0 bits (59), Expect = 6.5
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 133 HEEVVICRMRIGHTRATHGHLFKRAPPSTCRCGETLSVQ 171
H+ +CRM++G T T P TLSV
Sbjct: 98 HDGNYLCRMKLGETEVTKQEHLSVVKPL------TLSVH 130
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 26.7 bits (60), Expect = 8.7
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 163 RCGETLSVQHILTCTLHGHIRASLP 187
RCG T + L L HIR SLP
Sbjct: 56 RCG-TPYLAKKLNQELVNHIRKSLP 79
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 0.137 0.456
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,051,830
Number of extensions: 879554
Number of successful extensions: 641
Number of sequences better than 10.0: 1
Number of HSP's gapped: 640
Number of HSP's successfully gapped: 18
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
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: 56 (25.4 bits)