RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8376
(328 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 = 122 bits (309), Expect = 1e-34
Identities = 42/130 (32%), Positives = 65/130 (50%), Gaps = 6/130 (4%)
Query: 61 CYTDGSKTNTFTGGAYL---LNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFC 117
YTDGSK TG + ++L S++ AEL+AI L L +
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRA-- 59
Query: 118 FKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEM 177
+ I SDS+++L+AL+ + S L+ +I I+E+++ G +V W+P H GI NE
Sbjct: 60 -RKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNER 118
Query: 178 VDRAARNAVN 187
DR A+ A
Sbjct: 119 ADRLAKEAAK 128
>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 = 69.2 bits (170), Expect = 1e-14
Identities = 28/129 (21%), Positives = 51/129 (39%), Gaps = 10/129 (7%)
Query: 59 ILCYTDGS--KTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNF 116
+ YTDGS G Y+ + ++ + + AEL+A+ L ++
Sbjct: 4 VTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSG------ 57
Query: 117 CFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENE 176
+ I +DS+ + + I +I E+ +V W+P H GI NE
Sbjct: 58 --QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNE 115
Query: 177 MVDRAARNA 185
+ D+ A+
Sbjct: 116 LADKLAKQG 124
>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 = 48.9 bits (117), Expect = 2e-07
Identities = 30/132 (22%), Positives = 49/132 (37%), Gaps = 18/132 (13%)
Query: 62 YTDGSKTNTF---TGGAYLLNETVE----QFQLNQIASIYTAELMAIDLCLNSILMYIQN 114
TDGS G L + A+ AEL+A+ L ++ + +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLAL---LEALELALDL 57
Query: 115 NFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRE 174
K +I +DSK + + + +L I + S + F +P RE
Sbjct: 58 GL--KKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVP-----RE 110
Query: 175 -NEMVDRAARNA 185
NE+ DR A+ A
Sbjct: 111 GNEVADRLAKEA 122
>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 = 46.5 bits (111), Expect = 1e-06
Identities = 34/143 (23%), Positives = 52/143 (36%), Gaps = 24/143 (16%)
Query: 60 LCYTDGSKTNTFTGGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCF 118
+TDGS G A + +E L S AEL+A+ L
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALEL--------AKG 52
Query: 119 KDFVICSDSK---SSLQAL-------KFNLNDSILISKILLKIKEISSFGSQVSFLWIPS 168
K I +DS L AL F I ++ ++L++++ V+ + I +
Sbjct: 53 KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRA 112
Query: 169 HVG-----IRENEMVDRAARNAV 186
H G N D+AAR A
Sbjct: 113 HSGLPGPLALGNARADQAARQAA 135
>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 = 45.7 bits (109), Expect = 4e-06
Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 19/106 (17%)
Query: 96 AELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQAL--------KFNLNDSI----- 142
AEL A+ L I + VI +DS+ + + K S
Sbjct: 46 AELRAVIHALRLI---KEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA 102
Query: 143 ---LISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRAARNA 185
LI ++ ++E+ G +V F +P H GI NE DR A+
Sbjct: 103 NKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKG 148
>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 = 39.0 bits (92), Expect = 7e-04
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNA 185
QV++ W+ H G NE D A A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELANAA 137
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 38.5 bits (90), Expect = 0.001
Identities = 33/154 (21%), Positives = 56/154 (36%), Gaps = 30/154 (19%)
Query: 57 DKILCYTDG-SKTNTFTGG-AYLLNETVEQFQLNQIASIYT-------AELMAIDLCLNS 107
K+ +TDG N GG +L + +L S AEL A+ L +
Sbjct: 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKEL----SGGEGRTTNNRAELRALIEALEA 57
Query: 108 ILMYIQNNFCFKDFVICSDSKSSLQAL------------KFNLNDSILISKILLKIKEIS 155
+ + C + + +DSK ++ + K + + ++ E+
Sbjct: 58 LK---ELGAC--EVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELL 112
Query: 156 SFGSQVSFLWIPSHVGIRENEMVDRAARNAVNAR 189
V + W+ H G ENE D+ AR A A
Sbjct: 113 KRHELVFWEWVKGHAGHPENERADQLAREAARAA 146
>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 = 36.3 bits (85), Expect = 0.005
Identities = 31/144 (21%), Positives = 54/144 (37%), Gaps = 31/144 (21%)
Query: 61 CYTDGS---KTNTFTGGAYLL-NETVEQFQLNQIASIYT------AELMAIDLCLNSILM 110
Y DGS +T + G +L N +F + E+ + ++
Sbjct: 3 AYVDGSYNKETKVYGYGVVILKNGEEIKFSGSGNDPELASMRNVAGEIKG---AIKAMEY 59
Query: 111 YIQNNFCFKDFVICSD----SKSSLQALKFNLNDSI----LISKILLKIKEISSFGSQVS 162
++N K I D K + K N + + KI KIK +S
Sbjct: 60 AVENGI--KKITIYYDYEGIEKWATGEWKANKEGTKEYKEFMDKIKKKIK--------IS 109
Query: 163 FLWIPSHVGIRENEMVDRAARNAV 186
F+ + +H G + NE+ D+ A+ A+
Sbjct: 110 FVKVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 33.6 bits (78), Expect = 0.049
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVNARL 190
Q+ + W+ H G ENE D AR
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGAEEAT 144
>gnl|CDD|224409 COG1492, CobQ, Cobyric acid synthase [Coenzyme metabolism].
Length = 486
Score = 29.9 bits (68), Expect = 1.9
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 127 SKSSLQALKFNLNDSILISKILLKIKEISSFGSQV 161
+LQAL + S+ ++ +LLK S GSQV
Sbjct: 56 RAQALQALAAGIEPSVHMNPVLLKPC--SDTGSQV 88
>gnl|CDD|132144 TIGR03100, hydr1_PEP, exosortase A system-associated hydrolase 1.
This group of proteins are members of the alpha/beta
hydrolase superfamily. These proteins are generally
found in genomes containing the exosortase/PEP-CTERM
protein expoert system , specifically the type 1 variant
of this system described by the Genome Property
GenProp0652. When found in this context they are
invariably present in the vicinity of a second,
relatively unrelated enzyme (ortholog 2, TIGR03101) of
the same superfamily.
Length = 274
Score = 29.4 bits (66), Expect = 2.2
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 13/88 (14%)
Query: 200 KAHFKHIQFKR------WEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLR 253
+ +H + W ++ LG LR + + K + + + R++
Sbjct: 142 ASRIRHYYLGQLLSADFWRKLLSGEVNLGSSLRGLGDALLKARQKGDEVAHGG-LAERMK 200
Query: 254 IGHCLATHK----HLLERKDPPACEFCG 277
G L + +L D A EF
Sbjct: 201 AG--LERFQGPVLFILSGNDLTAQEFAD 226
>gnl|CDD|151410 pfam10963, DUF2765, Protein of unknown function (DUF2765). This
family of proteins has no known function.
Length = 82
Score = 27.2 bits (61), Expect = 3.0
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 8 VRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEIN 45
+R V +QKE + LL P M ++ +EE ++
Sbjct: 40 MRTVDPEQKEALKELLEVPGAAMQLAGAVNEEYAPDLE 77
>gnl|CDD|172536 PRK14042, PRK14042, pyruvate carboxylase subunit B; Provisional.
Length = 596
Score = 29.3 bits (65), Expect = 3.5
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 158 GSQVSFLWI---PSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQFKRWEEI 214
G Q FLW+ P V ++ +E+ D+ R++VN ++ + I +E+
Sbjct: 488 GQQSCFLWVDGVPEEVVVQHSELHDKIERSSVNNKIGPGDITVAIPGSIIAIHVSAGDEV 547
Query: 215 WRQNAVLGRQLRQIKTDVR 233
AVL + +++T+++
Sbjct: 548 KAGQAVLVIEAMKMETEIK 566
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 27.5 bits (60), Expect = 6.4
Identities = 40/147 (27%), Positives = 60/147 (40%), Gaps = 25/147 (17%)
Query: 57 DKILCYTDGSKTNTF--TGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQN 114
++I+ TDGS +G A+ ++E IA+ AEL A+ L I
Sbjct: 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELL------IAT 57
Query: 115 NFCFKDFVICSDSKSSLQAL----------KFNLNDS--ILISKILLKIKEISSF--GSQ 160
+ +I SDSK + +L K+ D +L +I I+EI S
Sbjct: 58 RHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEI---IQEIDSLMENRN 114
Query: 161 VSFLWIPSHVGIRENEMVDRAARNAVN 187
+ W+ +H G NE D AR A N
Sbjct: 115 IRMSWVNAHTGHPLNEAADSLARQAAN 141
>gnl|CDD|225323 COG2603, COG2603, Predicted ATPase [General function prediction
only].
Length = 334
Score = 27.9 bits (62), Expect = 7.5
Identities = 31/159 (19%), Positives = 53/159 (33%), Gaps = 23/159 (14%)
Query: 1 MDDYKLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKKDNKDKIL 60
DD + E+ K+Q Q L + E+ + F+++N IL
Sbjct: 42 NDDERQEIGTCYKKQ--------GQDAAKALGHALVCGEIRQQRLEASKAFQEENPVGIL 93
Query: 61 CYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSI-LMYIQNNFCFK 119
C G + + Q L A I ++ + L + + K
Sbjct: 94 CARGGLR------------SKIVQKWLGYAAGIDYPRVIGGEKALRTFAIQATIKEIAQK 141
Query: 120 DFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFG 158
DF++C + L L ++I + L SSFG
Sbjct: 142 DFILCGCTGCGKTELVEQLPNAIDLEG--LANHRGSSFG 178
>gnl|CDD|222052 pfam13335, Mg_chelatase_2, Magnesium chelatase, subunit ChlI. This
is a family of putative bacterial magnesium chelatase
subunit ChlI proteins. The domain lacks the P-loop
region present at the N-terminal of Mg_chelatase,
pfam01078.
Length = 97
Score = 26.3 bits (59), Expect = 8.3
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 206 IQFKRWEEIWRQNAVL-GRQLRQI 228
Q +R W+ NA L G +LR+
Sbjct: 18 RQAERQGGTWKLNAELSGAELRRF 41
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 0.135 0.409
Gapped
Lambda K H
0.267 0.0840 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,202,915
Number of extensions: 1512117
Number of successful extensions: 1273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1269
Number of HSP's successfully gapped: 27
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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: 59 (26.3 bits)