RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5071
(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 = 105 bits (264), Expect = 8e-28
Identities = 39/123 (31%), Positives = 59/123 (47%), Gaps = 5/123 (4%)
Query: 108 CFTDGSKTVNSTSCAYSI---GNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPS--TN 162
+TDGSK T ++I G ++KL SV +EL+AIL ++ +
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 163 FTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDI 222
T+ SDS +AL A+ + ++ PLV + E + G + W P H GI GNE D
Sbjct: 62 ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
Query: 223 AAR 225
A+
Sbjct: 122 LAK 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 = 55.3 bits (134), Expect = 1e-09
Identities = 28/128 (21%), Positives = 49/128 (38%), Gaps = 13/128 (10%)
Query: 104 DSVLCFTDGSKTVNS-TSCAYSIGNQVHAFKLNK-VNSVLSSELMAILLCVKNLIFLPST 161
++V +TDGS N A + + + +EL+A++ ++ L
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL---SGQ 58
Query: 162 NFTLISDSMSALLAISN-CKNDH---PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGN 217
+ +DS + I+N P+ + + E + W P H GI GN
Sbjct: 59 KVNIYTDSQYVIGGITNGWPTKSESKPIKNEI----WELLQKKHKVYIQWVPGHSGIPGN 114
Query: 218 ELVDIAAR 225
EL D A+
Sbjct: 115 ELADKLAK 122
>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 = 55.1 bits (133), Expect = 1e-09
Identities = 25/127 (19%), Positives = 45/127 (35%), Gaps = 11/127 (8%)
Query: 109 FTDGSKTVNSTSCAYSI------GNQVHAFKLNKVN-SVLSSELMAILLCVKNLIFLPST 161
TDGS N G + A L+ + +EL+A+L ++ + L
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 162 NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVD 221
+ +DS + I++ +L+ L ++ F P GNE+ D
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116
Query: 222 IAARNPI 228
A+
Sbjct: 117 RLAKEAA 123
>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 = 40.3 bits (95), Expect = 2e-04
Identities = 31/136 (22%), Positives = 46/136 (33%), Gaps = 21/136 (15%)
Query: 107 LCFTDGSKTVNSTSCA-YSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTL 165
FTDGS V A + + + L S +EL+A++ L +
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRA---LELAKGKPVNI 57
Query: 166 ISDS------MSALLAI-----SNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG- 213
+DS + AL I L SL+ +A K + + +H G
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQ-KAIQRPKPVAVIHIRAHSGL 116
Query: 214 ----ITGNELVDIAAR 225
GN D AAR
Sbjct: 117 PGPLALGNARADQAAR 132
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 35.8 bits (83), Expect = 0.011
Identities = 21/94 (22%), Positives = 31/94 (32%), Gaps = 12/94 (12%)
Query: 144 ELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTT---------WL 194
EL A++ ++ L L + TL +DS + I+ W
Sbjct: 47 ELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWE 106
Query: 195 EAKDCGKNL---NFVWCPSHCGITGNELVDIAAR 225
E + K + W H G NE D AR
Sbjct: 107 ELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 31.7 bits (73), Expect = 0.24
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 202 NLNFVWCPSHCGITGNELVDIAARNPI 228
++FV +H G NEL D A+ +
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 30.2 bits (69), Expect = 0.83
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 200 GKNLNFVWCPSHCGITGNELVDIAAR 225
+ + W H G GNE D A
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 199
Score = 29.8 bits (67), Expect = 1.6
Identities = 22/104 (21%), Positives = 35/104 (33%), Gaps = 17/104 (16%)
Query: 257 WDNVINNKLKRVKPLIVDWETSNRNSRYE-EVVITRLRIGHTRVTHDHLFKRDPRPTCGC 315
W I V ++V N+N E +VV T LF+ +
Sbjct: 100 WLQEIEQNCDDVCKVLV----GNKNDDPERKVVETEDAYKFAGQMGISLFETSAK----- 150
Query: 316 GDTLTVDHIFNCRTHLQIRASLPSPP------ALDNNPANIDSA 353
+ + V+ +FNC T L +RA + D +S
Sbjct: 151 -ENINVEEMFNCITELVLRAKKDNLAKQQQQQQNDVVKLPKNSK 193
>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
[Transcription].
Length = 1243
Score = 30.0 bits (67), Expect = 2.6
Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 14/102 (13%)
Query: 79 LDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVN 138
D K N+ ++H + Y+D +++ + AY IGN +
Sbjct: 754 FDLKVNLECKDTREHL---ESLIYND---------ESIQTIITAYLIGNPGNGKAALMRI 801
Query: 139 SVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK 180
S LS ++ VKNL FL NF ++ +L S
Sbjct: 802 SPLSRCSESLDEDVKNLCFLRDVNF--FNEFALSLYDKSLAL 841
>gnl|CDD|224489 COG1573, COG1573, Uracil-DNA glycosylase [DNA replication,
recombination, and repair].
Length = 202
Score = 29.3 bits (66), Expect = 2.7
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 12/64 (18%)
Query: 280 RNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPTCGCGDTLTVDHIFNCRTHLQIRASLPS 339
RYE+V IT + K P T + I CR L+ +L
Sbjct: 77 GGLRYEDVYITNV------------VKCRYPPGNRPPGDPTPEEIKACRPFLEAEIALIR 124
Query: 340 PPAL 343
P +
Sbjct: 125 PKVI 128
>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 = 28.3 bits (64), Expect = 3.9
Identities = 22/104 (21%), Positives = 38/104 (36%), Gaps = 26/104 (25%)
Query: 144 ELMAILLCVKNLIFL--PSTNFTLISDSMSALLAISN-----------------CKN-DH 183
EL A++ ++ + + T + +DS + ++ N D
Sbjct: 47 ELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDL 106
Query: 184 --PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAAR 225
L L+ E ++ G + F P H GI GNE D A+
Sbjct: 107 IKELDKLLE----ELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|200066 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle
type. This model finds organelle (chloroplast and
mitochondrial) ribosomal protein S4 as well as bacterial
ribosomal protein S4 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 200
Score = 28.4 bits (64), Expect = 4.7
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 4 VSKIGSCPSNPAHKELY-HTNINVNDFPPNKPKPLC-----VRIKDMSDFLPLITDSEFV 57
V ++G P+ A ++L H +I VN + P + IK+ S +PL+ ++
Sbjct: 96 VYRLGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKSKKIPLVKENLET 155
Query: 58 PFTRPRPPW 66
R P W
Sbjct: 156 NGQRNIPSW 164
>gnl|CDD|227889 COG5602, SIN3, Histone deacetylase complex, SIN3 component
[Chromatin structure and dynamics].
Length = 1163
Score = 28.3 bits (63), Expect = 7.7
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 338 PSPPALDNNPANIDSALMYLKAIGLY 363
PP + P ++ AL YL+ +
Sbjct: 116 SPPPRIPYRPLDVSDALSYLEKVKEQ 141
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
0.322 0.136 0.432
Gapped
Lambda K H
0.267 0.0642 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,262,774
Number of extensions: 1695953
Number of successful extensions: 1153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1149
Number of HSP's successfully gapped: 19
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 (21.9 bits)
S2: 60 (27.1 bits)