RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16039
(586 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 (263), Expect = 1e-26
Identities = 39/123 (31%), Positives = 59/123 (47%), Gaps = 5/123 (4%)
Query: 415 CFTDGSKTVNSTSCAYSI---GNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPS--TN 469
+TDGSK T ++I G ++KL SV +EL+AIL ++ +
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 470 FTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDI 529
T+ SDS +AL A+ + ++ PLV + E + G + W P H GI GNE D
Sbjct: 62 ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
Query: 530 AAR 532
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 = 56.5 bits (137), Expect = 1e-09
Identities = 28/128 (21%), Positives = 49/128 (38%), Gaps = 13/128 (10%)
Query: 411 DSVLCFTDGSKTVNS-TSCAYSIGNQVHAFKLNK-VNSVLSSELMAILLCVKNLIFLPST 468
++V +TDGS N A + + + +EL+A++ ++ L
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL---SGQ 58
Query: 469 NFTLISDSMSALLAISN-CKNDH---PLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGN 524
+ +DS + I+N P+ + + E + W P H GI GN
Sbjct: 59 KVNIYTDSQYVIGGITNGWPTKSESKPIKNEI----WELLQKKHKVYIQWVPGHSGIPGN 114
Query: 525 ELVDIAAR 532
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 = 55.8 bits (135), Expect = 1e-09
Identities = 25/127 (19%), Positives = 45/127 (35%), Gaps = 11/127 (8%)
Query: 416 FTDGSKTVNSTSCAYSI------GNQVHAFKLNKVN-SVLSSELMAILLCVKNLIFLPST 468
TDGS N G + A L+ + +EL+A+L ++ + L
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 469 NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVD 528
+ +DS + I++ +L+ L ++ F P GNE+ D
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116
Query: 529 IAARNPI 535
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 = 40.7 bits (96), Expect = 3e-04
Identities = 31/136 (22%), Positives = 46/136 (33%), Gaps = 21/136 (15%)
Query: 414 LCFTDGSKTVNSTSCA-YSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPSTNFTL 472
FTDGS V A + + + L S +EL+A++ L +
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRA---LELAKGKPVNI 57
Query: 473 ISDS------MSALLAI-----SNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCG- 520
+DS + AL I L SL+ +A K + + +H G
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQ-KAIQRPKPVAVIHIRAHSGL 116
Query: 521 ----ITGNELVDIAAR 532
GN D AAR
Sbjct: 117 PGPLALGNARADQAAR 132
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 37.3 bits (87), Expect = 0.013
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 141 LDEVLKWSQANGLIFSTDPQKSVCVLFSRARNPSFPKLYYSGVELKFANSTKFLGL 196
L + +WS+ +GL + P KS +L + + +G ++ + K+LG+
Sbjct: 166 LQRLQEWSKESGLKIN--PSKSKVMLIGN-KKKRLKDITLNGTPIEAVETFKYLGV 218
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 36.2 bits (84), Expect = 0.016
Identities = 21/94 (22%), Positives = 31/94 (32%), Gaps = 12/94 (12%)
Query: 451 ELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTT---------WL 501
EL A++ ++ L L + TL +DS + I+ W
Sbjct: 47 ELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWE 106
Query: 502 EAKDCGKNL---NFVWCPSHCGITGNELVDIAAR 532
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 = 32.1 bits (74), Expect = 0.31
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 509 NLNFVWCPSHCGITGNELVDIAARNPI 535
++FV +H G NEL D A+ +
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|220552 pfam10074, DUF2285, Uncharacterized conserved protein (DUF2285).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 106
Score = 29.9 bits (68), Expect = 1.0
Identities = 20/72 (27%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 55 TRIWRSLLTRSPLGLTRPQPVA-----THCCLGLTGRLS-ASVRQTARTPLSRADVGRDS 108
R+WR+L R+ R P L RL+ AS R A V D
Sbjct: 17 ARLWRALNGRAAGPDARALPAQQRRRLRLMLRALDARLAGASYRDIAEVLFGADRVAADE 76
Query: 109 LRSAADRKDVIR 120
+ +A R V R
Sbjct: 77 WKDSALRDRVRR 88
>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 = 30.6 bits (70), Expect = 1.1
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 507 GKNLNFVWCPSHCGITGNELVDIAAR 532
+ + W H G GNE D A
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|184234 PRK13677, PRK13677, hypothetical protein; Provisional.
Length = 125
Score = 30.0 bits (68), Expect = 1.3
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 6/44 (13%)
Query: 103 DVGRDSLRSAADRKDVIRFFFREEKREMGDKKILF-----RKTL 141
D+ R SLR A+ D+++ +FR++K E K + F RKT+
Sbjct: 15 DIDRYSLRQEAN-NDILKIYFRKDKGEFFAKSVKFKYPRQRKTV 57
>gnl|CDD|236824 PRK11024, PRK11024, colicin uptake protein TolR; Provisional.
Length = 141
Score = 29.7 bits (67), Expect = 2.1
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 261 DHILKRLNPIHNAGIRIATGALMTSPI 287
D I+K LN +H+AG++ + LMT PI
Sbjct: 117 DEIIKALNLLHSAGVK--SVGLMTQPI 141
>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
[Transcription].
Length = 1243
Score = 30.0 bits (67), Expect = 4.5
Identities = 24/102 (23%), Positives = 39/102 (38%), Gaps = 14/102 (13%)
Query: 386 LDNKDNIPPIVFQQHFHDLVTNKYSDSVLCFTDGSKTVNSTSCAYSIGNQVHAFKLNKVN 445
D K N+ ++H + Y+D +++ + AY IGN +
Sbjct: 754 FDLKVNLECKDTREHL---ESLIYND---------ESIQTIITAYLIGNPGNGKAALMRI 801
Query: 446 SVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCK 487
S LS ++ VKNL FL NF ++ +L S
Sbjct: 802 SPLSRCSESLDEDVKNLCFLRDVNF--FNEFALSLYDKSLAL 841
>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 = 29.2 bits (66), Expect = 4.5
Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 10/81 (12%)
Query: 299 LSLRRDKIIMRYVSKIGSCPSNPAHKELY-HTNINVNDFPPNKPKPLC-----VRIKDMS 352
L R D ++ R +G P+ A ++L H +I VN + P + IK+ S
Sbjct: 88 LESRLDNVVYR----LGFAPTRFAARQLVSHGHILVNGKKVDIPSYQVRPGDIISIKEKS 143
Query: 353 DFLPLITDSEFVPFTRPRPPW 373
+PL+ ++ R P W
Sbjct: 144 KKIPLVKENLETNGQRNIPSW 164
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 29.4 bits (65), Expect = 7.5
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 4 EVVTSRSILPLALLTIQAPENPSSCPPHRCPPCSS----TLSPYLSRHTDMLCRGTRIWR 59
E V + + P AL + Q P N + P HR ++ +L+P L+ D L G R+W
Sbjct: 2466 ETVPALAGTPPALASEQTPVNAGASPAHRVFNAATGKQASLTPVLNTLADGL--GARLWG 2523
Query: 60 SLLTRSPLG 68
++ ++ G
Sbjct: 2524 NVRYKASQG 2532
>gnl|CDD|227881 COG5594, COG5594, Uncharacterized integral membrane protein
[Function unknown].
Length = 827
Score = 28.9 bits (65), Expect = 8.2
Identities = 13/83 (15%), Positives = 24/83 (28%), Gaps = 9/83 (10%)
Query: 262 HILKRLNPIHNAGIRIATGALMTSPICSLYVESGIGPLSLRRDKIIMRYVSKIGSCPSNP 321
+ + + + I + LY E RDKI+ + + +
Sbjct: 225 ELKELFDKLKVGEIDSDVLCRDLGTLQELYKE---------RDKILKKLEKALNELLNKL 275
Query: 322 AHKELYHTNINVNDFPPNKPKPL 344
K TN P++ K
Sbjct: 276 LKKSHLKTNKKSGKLTPSRKKEF 298
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
0.323 0.137 0.426
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,292,973
Number of extensions: 2791928
Number of successful extensions: 2061
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2056
Number of HSP's successfully gapped: 18
Length of query: 586
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 484
Effective length of database: 6,413,494
Effective search space: 3104131096
Effective search space used: 3104131096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 62 (27.9 bits)