RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14646
(366 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 = 63.0 bits (154), Expect = 2e-12
Identities = 36/152 (23%), Positives = 54/152 (35%), Gaps = 44/152 (28%)
Query: 50 ETGVGCALTIPQLNETKR-FALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNK 108
E G I + R + L + S+F AEL +I
Sbjct: 10 EGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAI------------------------ 45
Query: 109 HELKDKLLQQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISNLYHPNPLVKKIQ 168
+ LQ RKI I SDS ++ +A+ + +PLV +I+
Sbjct: 46 ----LEALQLALREGRR------------ARKITIFSDSQAALKALRSPRSSSPLVLRIR 89
Query: 169 ---EEYSNSQANIKFLWCPSHVSISGNERAEE 197
E +N ++ W P H I GNERA+
Sbjct: 90 KAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
>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 = 44.6 bits (106), Expect = 8e-06
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 134 KELDTRKILIISDSLSSFQAISNLYH----PNPLVKKIQEEYSNSQANIKFLWCPSHVSI 189
+ L +K+ I +DS I+N + P+ +I E + W P H I
Sbjct: 53 EALSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHK-VYIQWVPGHSGI 111
Query: 190 SGNERAEE 197
GNE A++
Sbjct: 112 PGNELADK 119
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 31.6 bits (72), Expect = 0.27
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 15/87 (17%)
Query: 127 LQSLNHVKELDTRKILIISDSLSSFQAISNLYHPNPL---VKKIQEEYSNSQA------- 176
+++L +KEL ++ + +DS + I+ ++ N
Sbjct: 52 IEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDEL 111
Query: 177 -----NIKFLWCPSHVSISGNERAEEC 198
+ + W H NERA++
Sbjct: 112 LKRHELVFWEWVKGHAGHPENERADQL 138
>gnl|CDD|219044 pfam06470, SMC_hinge, SMC proteins Flexible Hinge Domain. This
family represents the hinge region of the SMC
(Structural Maintenance of Chromosomes) family of
proteins. The hinge region is responsible for formation
of the DNA interacting dimer. It is also possible that
the precise structure of it is an essential determinant
of the specificity of the DNA-protein interaction.
Length = 117
Score = 30.7 bits (70), Expect = 0.43
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLKRNN 361
LG L I+ D+ ++ + FLK+NN
Sbjct: 26 LGGRLQAIVVDDEETAKAAIEFLKKNN 52
>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 = 31.0 bits (71), Expect = 0.43
Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 22/89 (24%)
Query: 127 LQSLNHVKELDTRKILIISDS--------------------LSSFQAISNLYHPNPLVKK 166
L+ + V E K++I +DS S + ++N L K
Sbjct: 55 LRLIKEVGE-GLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKL 113
Query: 167 IQEEYSNSQANIKFLWCPSHVSISGNERA 195
++E +KF P H I GNE A
Sbjct: 114 LEELE-ERGIRVKFWHVPGHSGIYGNEEA 141
>gnl|CDD|214944 smart00968, SMC_hinge, SMC proteins Flexible Hinge Domain. This
entry represents the hinge region of the SMC (Structural
Maintenance of Chromosomes) family of proteins. The
hinge region is responsible for formation of the DNA
interacting dimer. It is also possible that the precise
structure of it is an essential determinant of the
specificity of the DNA-protein interaction.
Length = 120
Score = 29.9 bits (68), Expect = 0.90
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 335 LGNSLSNILSDNPDSISTLMRFLKRNN 361
LG L ++ D ++ + FLK+N
Sbjct: 25 LGGRLQAVVVDTEETAKKAIEFLKKNR 51
>gnl|CDD|218876 pfam06054, CoiA, Competence protein CoiA-like family. Many of the
members of this family are described as transcription
factors. CoiA falls within a competence-specific operon
in Streptococcus. CoiA is an uncharacterized protein.
Length = 348
Score = 30.9 bits (70), Expect = 1.00
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 286 RLRIGHTKITHSHLFKREERPECDTCHEPVTVEHL 320
L+ G KI H F + +C E + EHL
Sbjct: 35 ILKQGQIKIPH---FAHKSLKDCAFSSENESAEHL 66
>gnl|CDD|198419 cd10461, PUB_UBA_plant, PNGase/UBA or UBX (PUB) domain of plant
Ubiquitin-associated (UBA) domain containing proteins.
The PUB domain functions as a p97 (also known as
valosin-containing protein or VCP) adaptor by
interacting with the D1 and/or D2 ATPase domains. The
type II AAA+ ATPase p97 is involved in a variety of
cellular processes such as the deglycosylation of ERAD
substrates, membrane fusion, transcription factor
activation and cell cycle regulation through
differential binding to specific adaptor proteins. The
UBA domain, along with UBL (ubiquitin-like) domain, has
been implicated in proteasomal degradation by
associating with substrates destined for degradation as
well as with subunits of the proteasome, thus regulating
protein turnover. This family contains only plant UBA
domain-containing proteins.
Length = 107
Score = 29.3 bits (66), Expect = 1.00
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 232 KNLHYGSDEATSVKWNTVWTSI-----NPNENKLRRIK 264
K H +A + T+ T + NP+E K RRI+
Sbjct: 5 KKAHKDDPDAVKTAFQTLLTYLGNVAKNPDEEKFRRIR 42
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found
in plants and appears to be part of a retrotransposon.
Length = 88
Score = 28.7 bits (65), Expect = 1.2
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 130 LNHVKELDTRKILIISDSLSSFQAISNLYHPN----PLVKKIQE 169
L EL R++++ SDS Q I Y L+++I++
Sbjct: 14 LQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRK 57
>gnl|CDD|153401 cd08032, LARP_7, La RNA-binding domain of La-related protein 7.
LARP7 is a component of the 7SK snRNP, a key factor in
the regulation of RNA polymerase II transcription. 7SK
functionality is dependent on the presence of LARP7,
which is thought to stabilize the 7SK RNA by interacting
with its 3' end. The release of 7SK RNA from
P-TEFb/HEXIM/7SK complexes activates the
cyclin-dependent kinase P-TEFb, which in turn
phosphorylates the C-terminal domain of RNA pol II and
mediates a transition into productive transcription
elongation.
Length = 82
Score = 28.0 bits (62), Expect = 1.8
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 6/54 (11%)
Query: 96 DRDSSIDIFFNNKHELKDKLLQQI------AYVDINSLQSLNHVKELDTRKILI 143
D +D +F + + KD+ L++ Y+DI+ L S N +K+L T LI
Sbjct: 8 DIAKQVDFWFGDVNLHKDRFLREQIEKSRDGYIDISLLVSFNKMKKLTTDGKLI 61
>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 = 29.0 bits (66), Expect = 2.0
Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 20/87 (22%)
Query: 127 LQSLNHVKELDTRKILIISDSLSSFQAISNLYH---------------PNP-LVKKIQEE 170
+++L +KE +L+ +DS I+ H N L +++
Sbjct: 50 IEALEALKE--PCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQELDAL 107
Query: 171 YSNSQANIKFLWCPSHVSISGNERAEE 197
+ Q + + W H GNERA+E
Sbjct: 108 LAKHQ--VTWHWVKGHAGHPGNERADE 132
>gnl|CDD|185187 PRK15287, PRK15287, putative minor fimbrial subunit StfF;
Provisional.
Length = 158
Score = 29.3 bits (65), Expect = 2.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 6/31 (19%)
Query: 77 FHAELFSIPLHLSLTNCTIDRDSSIDIFFNN 107
FH L S P NCTI+ D +ID+ F N
Sbjct: 24 FHGTLISPP------NCTINNDQTIDVKFGN 48
>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 = 28.1 bits (63), Expect = 3.6
Identities = 18/72 (25%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 127 LQSLNHVKELDTRKILIISDSLSSFQAISN---LYHPNPLVKKIQEEYSNSQANIKFLWC 183
L++L +L +K++I +DS I++ + N L+ + +I+F
Sbjct: 48 LEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRF--- 104
Query: 184 PSHVSISGNERA 195
HV GNE A
Sbjct: 105 -EHVPREGNEVA 115
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 28.4 bits (64), Expect = 4.3
Identities = 16/67 (23%), Positives = 29/67 (43%)
Query: 90 LTNCTIDRDSSIDIFFNNKHELKDKLLQQIAYVDINSLQSLNHVKELDTRKILIISDSLS 149
L I+ D I I K E + + V++ S +LN L ++I+I ++L
Sbjct: 148 LKKLNINLDQKILIIVPEKTENLYLSTRNLKNVELISADTLNIKSLLKAKQIIITKEALK 207
Query: 150 SFQAISN 156
+ + N
Sbjct: 208 IIEEVYN 214
>gnl|CDD|233913 TIGR02536, eut_hyp, ethanolamine utilization protein. This family
of proteins is found in operons for the polyhedral
organelle-based degradation of ethanolamine. This family
is not found in proteobacterial species which otherwise
have the same suite of genes in the eut operon.
Proteobacteria have two genes that are not found in
non-proteobacteria which may complement this genes
function, a phosphotransacetylase (pfam01515) and the
EutJ protein (TIGR02529) of unknown function.
Length = 207
Score = 28.3 bits (63), Expect = 5.9
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 95 IDRDSSIDIFFNNKHELKDKLLQQIAYVDINSLQSLNHVKELDTRKILIISD-SLSSFQA 153
++ I ++KH + +++L++ D++ + S E IL++S S+
Sbjct: 18 LEEKKYIVALGDSKHAIPEEMLKEF---DVSWVTS-----EQKLADILLVSRLSIKELNN 69
Query: 154 ISNLYHPNPLVKKI 167
IS+ N K I
Sbjct: 70 ISHGQETNEKEKFI 83
>gnl|CDD|220058 pfam08885, GSCFA, GSCFA family. This family of proteins are
functionally uncharacterized. They have been named GSCFA
after a highly conserved N-terminal motif in the
alignment. Distant similarity to the pfam00657 lipases
suggests these proteins are likely to be enzymes.
Length = 251
Score = 27.9 bits (63), Expect = 8.3
Identities = 8/54 (14%), Positives = 16/54 (29%), Gaps = 7/54 (12%)
Query: 156 NLYHPNPLVKKIQEEYSNSQANIKFLW-------CPSHVSISGNERAEECYSNY 202
N+Y P +++ ++ +W S G EE +
Sbjct: 35 NIYTPRSILQLLRRALGKKSFTEADIWEQDGRWHDFLAHSPFGFASEEELLAAR 88
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
0.319 0.133 0.405
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,075,956
Number of extensions: 1679107
Number of successful extensions: 1407
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1403
Number of HSP's successfully gapped: 30
Length of query: 366
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 268
Effective length of database: 6,590,910
Effective search space: 1766363880
Effective search space used: 1766363880
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: 60 (26.8 bits)