RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2213
(194 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 = 77.3 bits (191), Expect = 1e-18
Identities = 25/64 (39%), Positives = 38/64 (59%)
Query: 8 KFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVD 67
K I SDS++ L AL +P +++P+V I +L G ++ W P H+GI+GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 68 RAAR 71
R A+
Sbjct: 121 RLAK 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 = 57.3 bits (139), Expect = 6e-11
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 4 LPKEKFVIISDSKST----LLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTG 59
L +K I +DS+ S + PI + I +LL ++ W P H+G
Sbjct: 55 LSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPGHSG 110
Query: 60 IQGNEAVDRAAR 71
I GNE D+ A+
Sbjct: 111 IPGNELADKLAK 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 = 37.9 bits (89), Expect = 7e-04
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 41 DLLCCGKQLAFLWCPSHTGIQGNEAVDRAAR 71
D L Q+ + W H G GNE D A
Sbjct: 105 DALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>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 = 37.2 bits (87), Expect = 0.001
Identities = 17/84 (20%), Positives = 28/84 (33%), Gaps = 23/84 (27%)
Query: 7 EKFVIISDSK---STLLAL-----------SNPSNTNPIVSLIHSCWSDLLCCGKQLAFL 52
+ I +DS L AL P ++ + + K +A +
Sbjct: 53 KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQL----QKAIQRPKPVAVI 108
Query: 53 WCPSHTG-----IQGNEAVDRAAR 71
+H+G GN D+AAR
Sbjct: 109 HIRAHSGLPGPLALGNARADQAAR 132
>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 = 34.6 bits (80), Expect = 0.009
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 7 EKFVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAV 66
+K +I +DSK + +++ S +L+ LL + F P GNE
Sbjct: 60 KKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVA 115
Query: 67 DRAARNP 73
DR A+
Sbjct: 116 DRLAKEA 122
>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 = 0.035
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 51 FLWCPSHTGIQGNEAVDRAARN 72
F+ +H+G + NE D+ A+
Sbjct: 110 FVKVKAHSGDKYNELADKLAKK 131
>gnl|CDD|237244 PRK12876, ubiA, prenyltransferase; Reviewed.
Length = 300
Score = 32.4 bits (74), Expect = 0.11
Identities = 25/79 (31%), Positives = 33/79 (41%), Gaps = 10/79 (12%)
Query: 9 FVIISDSKSTLLALSNPSNTNPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDR 68
F + S ST+ ALS P + + SL + G AF C GI N+ +D
Sbjct: 18 FSALFLSASTVFALSLPEISFSLFSL--GGIKTISLGG--SAFF-CARTVGIIVNQIIDC 72
Query: 69 A--ARNPSAS---LPPLKL 82
A +NP S LP L
Sbjct: 73 AIDKKNPRTSSRVLPAKLL 91
>gnl|CDD|183716 PRK12744, PRK12744, short chain dehydrogenase; Provisional.
Length = 257
Score = 30.5 bits (69), Expect = 0.39
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 62 GNEAVDRAARNPSAS----LPPLKLCSPEDFKPFIRKLIKDLW 100
E + A + +A+ L ED PFIR L+ D W
Sbjct: 199 PQEGAEAVAYHKTAAALSPFSKTGLTDIEDIVPFIRFLVTDGW 241
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.0 bits (68), Expect = 0.49
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 53 WCPSHTGIQGNEAVDRAAR 71
W H G NE D+ AR
Sbjct: 122 WVKGHAGHPENERADQLAR 140
>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 = 29.1 bits (66), Expect = 0.84
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 16/83 (19%)
Query: 5 PKEKFVIISDSKSTLLALSN-----------PSNTNPIV-----SLIHSCWSDLLCCGKQ 48
K VI +DS+ + ++ S P+ + +L G +
Sbjct: 64 GLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEELEERGIR 123
Query: 49 LAFLWCPSHTGIQGNEAVDRAAR 71
+ F P H+GI GNE DR A+
Sbjct: 124 VKFWHVPGHSGIYGNEEADRLAK 146
>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 = 1.6
Identities = 9/10 (90%), Positives = 9/10 (90%), Gaps = 1/10 (10%)
Query: 142 IGHTR-ATHG 150
IGHTR ATHG
Sbjct: 68 IGHTRWATHG 77
>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 = 28.7 bits (65), Expect = 1.8
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 84 SPEDF-KPFIRKLIKDLW 100
+P +F KPF+ K IKD W
Sbjct: 250 TPMNFNKPFLSKDIKDFW 267
>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 = 2.5
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 133 EEVVICRMRIGHTR-ATHG 150
+E +I + I HTR ATHG
Sbjct: 61 KEPLIGGVGIAHTRWATHG 79
>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 = 26.6 bits (59), Expect = 3.7
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 7/48 (14%)
Query: 52 LWCPSHTGIQGN-------EAVDRAARNPSASLPPLKLCSPEDFKPFI 92
+WCP T I G V+ A R+ L + E+ ++
Sbjct: 49 MWCPGWTPITGESRTRSRSGVVEHAVRDFVQKALQAGLITEEEANAWL 96
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 26.7 bits (59), Expect = 4.9
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 56 SHTGIQGNEAVDRAA 70
+H+GI+GNEA D A
Sbjct: 127 AHSGIEGNEAADMLA 141
>gnl|CDD|225548 COG3002, COG3002, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 880
Score = 27.6 bits (61), Expect = 4.9
Identities = 21/104 (20%), Positives = 33/104 (31%), Gaps = 7/104 (6%)
Query: 91 FIRKLIKDLWQQSWSSIPNSNKLKSIKPIIGPWPSSDRQNRYEEVVICRMRIGHTRATHG 150
L K LW ++W + I P+ ++ + + +R R
Sbjct: 343 INASLFKKLWLRAWEITYQRQLFQKITSAQQSEPNQEKSPKAQAAFCIDVRSEPFRR--- 399
Query: 151 HLFKRAPPSTCGCGEILSVQHILTCALH-GHIRASLPT--PPAL 191
HL + P T G + I L H SLP P+
Sbjct: 400 HLEAQGPFETIGIAGFFGLP-IAYQELGTEHSHPSLPVLLKPSN 442
>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 = 5.0
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 75 ASLPPLKLCSPEDFKPFIR 93
ASL K+ PE KPF +
Sbjct: 38 ASLGSKKIIDPEALKPFSK 56
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 27.4 bits (61), Expect = 5.9
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 86 EDFKPF-IRKLIKDLWQQSW---SSIPNSNKLKSIKPIIGPW 123
+ +PF IR I + + W SS N+ + S+KP+I W
Sbjct: 351 KGREPFSIRDWILNEQKNGWLFISS--NAQQHASLKPLISMW 390
>gnl|CDD|132728 cd06930, NR_LBD_F2, Ligand-binding domain of nuclear receptor
family 2. Ligand-binding domain (LBD) of nuclear
receptor (NR) family 2: This is one of the major
subfamily of nuclear receptors, including some well
known nuclear receptors such as glucocorticoid receptor
(GR), mineralocorticoid receptor (MR), estrogen
receptor (ER), progesterone receptor (PR), and androgen
receptor (AR), other related receptors. Nuclear
receptors form a superfamily of ligand-activated
transcription regulators, which regulate various
physiological functions, from development,
reproduction, to homeostasis and metabolism in animals
(metazoans). The family contains not only receptors for
known ligands but also orphan receptors for which
ligands do not exist or have not been identified. NRs
share a common structural organization with a central
well conserved DNA binding domain (DBD), a variable
N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 165
Score = 26.0 bits (58), Expect = 8.9
Identities = 6/31 (19%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 32 VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQG 62
++L+ + W++LL L H +
Sbjct: 34 LTLLQNSWAELLL----LGLAQRSVHFELSE 60
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 27.0 bits (60), Expect = 9.1
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 10/43 (23%)
Query: 112 KLKSIKPIIGPW----------PSSDRQNRYEEVVICRMRIGH 144
K K IKPIIG P ++ RY VV+ + G+
Sbjct: 55 KGKGIKPIIGNEMYVINGSIDDPQPKKEKRYHLVVLAKNATGY 97
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 26.7 bits (59), Expect = 9.9
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 86 EDFKPFIRKLIKDLWQ-----QSWSSIPNSNKLKSIKP 118
D K + + ++Q W IP S K+ +KP
Sbjct: 438 HDLKRWRNIGYEAVYQYDERLSKWLGIPLSIKVTCVKP 475
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
0.320 0.134 0.438
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: 9,757,746
Number of extensions: 855742
Number of successful extensions: 672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 670
Number of HSP's successfully gapped: 24
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
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 (21.8 bits)
S2: 56 (25.4 bits)