RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3458
(151 letters)
>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 = 185 bits (471), Expect = 4e-61
Identities = 65/149 (43%), Positives = 96/149 (64%), Gaps = 7/149 (4%)
Query: 8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRV-TNNNAEIQGAIHALKQAKS 66
VV+TDGAC NG+ GA AGYGVYFG +P NV+ ++ G TN AE++ IHAL+ K
Sbjct: 1 VVYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKE 60
Query: 67 ANID--RVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQME-- 122
++ I +DS++++ V EW+PKW+ NGW+ + GKPV NK+ ++EL + ++E
Sbjct: 61 VGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEELEER 120
Query: 123 --SVKWEFVPGHGNSHGNMKADEMARDAA 149
VK+ VPGH +GN +AD +A+ A
Sbjct: 121 GIRVKFWHVPGHSGIYGNEEADRLAKKGA 149
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 125 bits (317), Expect = 7e-38
Identities = 54/144 (37%), Positives = 81/144 (56%), Gaps = 3/144 (2%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDGAC N G G+G + GR TNN AE++ I AL+ K
Sbjct: 3 KVEIFTDGACLGNPGPG---GWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALK 59
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
V + +DS+++++ + W+ KW+ NGW+ AD KPV+NK+ +EL + + E V
Sbjct: 60 ELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVF 119
Query: 126 WEFVPGHGNSHGNMKADEMARDAA 149
WE+V GH N +AD++AR+AA
Sbjct: 120 WEWVKGHAGHPENERADQLAREAA 143
>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 = 115 bits (291), Expect = 6e-34
Identities = 49/143 (34%), Positives = 71/143 (49%), Gaps = 6/143 (4%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
+ ++TDGAC N G G+ + TNN E+ I AL+ K
Sbjct: 2 ITIYTDGACLGNPGPG---GWAAILRYGDHEKELSGGEAGTTNNRMELTAVIEALEALKE 58
Query: 67 ANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKW 126
V + +DSQ++I + +W+ W+ NGW+ ADGKPV+N + QEL + V W
Sbjct: 59 P--CPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQELDALL-AKHQVTW 115
Query: 127 EFVPGHGNSHGNMKADEMARDAA 149
+V GH GN +ADE+A AA
Sbjct: 116 HWVKGHAGHPGNERADELANAAA 138
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 98.0 bits (245), Expect = 6e-27
Identities = 52/148 (35%), Positives = 76/148 (51%), Gaps = 12/148 (8%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
V ++TDGAC N G G+G Y G L+ +T TNN E+ AI AL
Sbjct: 2 KQVEIYTDGACLGNPGPG---GWGAILRYKGHEKELSGGEALT---TNNRMELMAAIEAL 55
Query: 62 KQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQM 121
+ K V + +DSQ++ + + EW+ W+ NGW+ AD KPV+N + Q L + +
Sbjct: 56 EALKEPC--EVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KR 112
Query: 122 ESVKWEFVPGHGNSHGNMKADEMARDAA 149
+KW +V GH N + DE+AR A
Sbjct: 113 HQIKWHWVKGHAGHPENERCDELARAGA 140
>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 = 93.1 bits (232), Expect = 3e-25
Identities = 47/147 (31%), Positives = 70/147 (47%), Gaps = 23/147 (15%)
Query: 4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
V V+TDG+C N G AGY G+ K TN AE+ I AL+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGG-AGYVTDGGKQ-----RSKPLPGTTNQRAELLALIEALEA 54
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWR-KADGKPVQNKEELQELLHQIGQME 122
+V I +DSQ++I + +NGW K++ KP++N+ + ELL +
Sbjct: 55 LSGQ---KVNIYTDSQYVIGGI--------TNGWPTKSESKPIKNE--IWELLQK---KH 98
Query: 123 SVKWEFVPGHGNSHGNMKADEMARDAA 149
V ++VPGH GN AD++A+ A
Sbjct: 99 KVYIQWVPGHSGIPGNELADKLAKQGA 125
>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 = 85.5 bits (212), Expect = 2e-22
Identities = 36/142 (25%), Positives = 66/142 (46%), Gaps = 21/142 (14%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRV-TNNNAEIQGAIHALKQAKSA 67
TDG+C N AG G ++ AG ++ TNN AE+ + AL+ A
Sbjct: 1 NTDGSCKGNPG---PAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDL 57
Query: 68 NIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWE 127
+ ++ I++DS++++ + W W+ +N L ++L + + +++E
Sbjct: 58 GLKKLIIETDSKYVVDLINSWSKGWK------------KNNLLLWDILLLLSKFIDIRFE 105
Query: 128 FVPGHGNSHGNMKADEMARDAA 149
VP GN AD +A++AA
Sbjct: 106 HVPREGNE----VADRLAKEAA 123
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 70.3 bits (172), Expect = 3e-16
Identities = 47/152 (30%), Positives = 71/152 (46%), Gaps = 16/152 (10%)
Query: 5 NHVVVFTDGACPRN--GKVGASAGYGVYFGENNPL--NVAGKVTGRVTNNNAEIQGAIHA 60
++ DGA P N G V G VY E + + V N E+ I A
Sbjct: 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVY-DEAGEIVDEQSITVNRYTDNAELELLALIEA 61
Query: 61 LKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQ 120
L+ A+ ++ I SDS + ++ EW+ W+ GWRK+D KPV N ++L Q+ +
Sbjct: 62 LEYARDGDV----IYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVAN----RDLWQQVDE 113
Query: 121 MESVKW---EFVPGHGNSHGNMKADEMARDAA 149
+ + K+ E V H GN AD +A+ AA
Sbjct: 114 LRARKYVEVEKVTAHSGIEGNEAADMLAQAAA 145
>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 = 66.5 bits (163), Expect = 6e-15
Identities = 36/145 (24%), Positives = 64/145 (44%), Gaps = 21/145 (14%)
Query: 8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK-- 65
V++TDG+ K+ G G ++ + K+ + +AE+ + AL+ A
Sbjct: 1 VIYTDGS-----KLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE 55
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNG-WRKADGKPVQNKEELQELLHQIGQMESV 124
++ I SDSQ +K ++ RKA ++EL + ++ +
Sbjct: 56 GRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKA----------IRELANHGVKV-RL 104
Query: 125 KWEFVPGHGNSHGNMKADEMARDAA 149
W VPGH GN +AD +A++AA
Sbjct: 105 HW--VPGHSGIEGNERADRLAKEAA 127
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. 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. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 63.3 bits (155), Expect = 1e-13
Identities = 35/148 (23%), Positives = 56/148 (37%), Gaps = 26/148 (17%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
++ DGA N A AG + + L + + TNN AE + I L+ A
Sbjct: 1 WTLYFDGASRGNPG-PAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALE 59
Query: 67 ANIDRVCIKSDSQFMIKCVQ-EWMPKWQSNGWRKADGKPVQNKEELQELLHQI----GQM 121
I ++ I DSQ ++ +Q E+ K E L L + +
Sbjct: 60 LGIKKLEIYGDSQLVVNQIQGEYEVK----------------NERLAPYLEEARELLKKF 103
Query: 122 ESVKWEFVPGHGNSHGNMKADEMARDAA 149
E V+ +++P N AD +A A
Sbjct: 104 EEVEIKWIPREENKE----ADALANQAL 127
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 60.6 bits (146), Expect = 2e-12
Identities = 46/146 (31%), Positives = 74/146 (50%), Gaps = 8/146 (5%)
Query: 4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
+N ++ TDG+ N +G+ Y EN + + TNN AE+ A+ L
Sbjct: 3 NNEIIAATDGSSLANP---GPSGWAWYVDENTWDSGGWDIA---TNNIAELT-AVRELLI 55
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMES 123
A + I SDS+++I + +W+ W+ WRKADGKPV N+E +QE + + + +
Sbjct: 56 ATRHTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQE-IDSLMENRN 114
Query: 124 VKWEFVPGHGNSHGNMKADEMARDAA 149
++ +V H N AD +AR AA
Sbjct: 115 IRMSWVNAHTGHPLNEAADSLARQAA 140
>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 = 54.6 bits (132), Expect = 3e-10
Identities = 38/149 (25%), Positives = 58/149 (38%), Gaps = 21/149 (14%)
Query: 8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA--K 65
VFTDG+ AGY V G + + + AE+ I AL+ A K
Sbjct: 1 TVFTDGSS-----FVRKAGYAVVTGPDVL--EIATLPYGTSAQRAELIALIRALELAKGK 53
Query: 66 SANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVK 125
NI +DS + + W+ G+ GKP+ + +L I + + V
Sbjct: 54 PVNIY-----TDSAYAFGILHALETIWKERGFLT--GKPIALASLILQLQKAIQRPKPVA 106
Query: 126 WEFVPGHGN-----SHGNMKADEMARDAA 149
+ H + GN +AD+ AR AA
Sbjct: 107 VIHIRAHSGLPGPLALGNARADQAARQAA 135
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 43.4 bits (103), Expect = 1e-05
Identities = 47/147 (31%), Positives = 64/147 (43%), Gaps = 25/147 (17%)
Query: 7 VVVFTDGACPRNGKVGASAGYG-VYFGENN--PLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
VVV DG N AGYG V + + L + GR TNN AE +G I L+
Sbjct: 3 VVVEADGGSRGNPGP---AGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEA 59
Query: 64 AKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWR--KADGKPVQNKEELQELLHQIGQM 121
A V ++ DS K V E M S W+ D KP+ + +EL Q G
Sbjct: 60 AAELGATEVEVRMDS----KLVVEQM----SGRWKVKHPDMKPLA--AQARELASQFG-- 107
Query: 122 ESVKWEFVPGHGNSHGNMKADEMARDA 148
V + ++P N+H AD +A +A
Sbjct: 108 -RVTYTWIPRARNAH----ADRLANEA 129
>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 = 40.9 bits (97), Expect = 3e-05
Identities = 31/114 (27%), Positives = 48/114 (42%), Gaps = 27/114 (23%)
Query: 38 NVAGKVTGRVTNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGW 97
NVAG EI+GAI A++ A I ++ I D E + KW + G
Sbjct: 45 NVAG-----------EIKGAIKAMEYAVENGIKKITIYYD--------YEGIEKW-ATGE 84
Query: 98 RKADGKPVQN--KEELQELLHQIGQMESVKWEFVPGHGNSHGNMKADEMARDAA 149
KA+ K KE + ++ +I + + V H N AD++A+ A
Sbjct: 85 WKAN-KEGTKEYKEFMDKIKKKI----KISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 40.2 bits (95), Expect = 3e-05
Identities = 25/109 (22%), Positives = 45/109 (41%), Gaps = 26/109 (23%)
Query: 48 TNNNAEIQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQ-EWMPKWQSNGWRKADGKPVQ 106
+ AE + + L+ A I R+ ++SDSQ +++ +Q E+
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEA---------------- 44
Query: 107 NKEELQELLHQIGQM----ESVKWEFVPGHGNSHGNMKADEMARDAAGW 151
+ L LL +I ++ +SV VP N AD +A+ A+
Sbjct: 45 -RSRLAALLREIRKLLKKFDSVSVSHVPRECNRV----ADALAKLASAS 88
>gnl|CDD|139967 PRK13907, rnhA, ribonuclease H; Provisional.
Length = 128
Score = 35.8 bits (82), Expect = 0.002
Identities = 39/141 (27%), Positives = 64/141 (45%), Gaps = 21/141 (14%)
Query: 9 VFTDGACPRNGKVGASAGYGVYF-GENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSA 67
V+ DGA G G S G GV+ G + ++ + G ++N+ AE + ALK
Sbjct: 4 VYIDGA--SKGNPGPS-GAGVFIKGVQPAVQLSLPL-GTMSNHEAEYHALLAALKYCTEH 59
Query: 68 NIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQMESVKWE 127
N + V ++DSQ + + V++ K + P+ L+E L I + +
Sbjct: 60 NYNIVSFRTDSQLVERAVEKEYAKNKMFA-------PL-----LEEALQYIKSFDLFFIK 107
Query: 128 FVPGHGNSHGNMKADEMARDA 148
++P S N ADE+AR A
Sbjct: 108 WIP----SSQNKVADELARKA 124
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 35.7 bits (83), Expect = 0.005
Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 14/92 (15%)
Query: 61 LKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKPVQNKEELQELLHQIGQ 120
L+QA D + + I+ Q RK GK + +++E ++ + +
Sbjct: 210 LEQALELGPDHLSL---YSLAIE---PGTKFAQ----RKIKGKALPDEDEKADMYELVEE 259
Query: 121 -MESVKWEFVPGHGNSHGNMKADEMARDAAGW 151
+E + + S+ E + W
Sbjct: 260 LLEKAGYRQ---YEISNFAKPGGECRHNLQYW 288
>gnl|CDD|224133 COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase
[Cell envelope biogenesis, outer membrane].
Length = 247
Score = 28.4 bits (64), Expect = 1.5
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 59 HALKQAKSANIDRVCIKSDSQFMIKCVQE 87
++A + DRV + +D + + + VQ
Sbjct: 33 RVAERALKSGADRVVVATDDERIAEAVQA 61
>gnl|CDD|221472 pfam12228, DUF3604, Protein of unknown function (DUF3604). This
family of proteins is found in bacteria. Proteins in
this family are typically between 621 and 693 amino
acids in length.
Length = 592
Score = 28.4 bits (64), Expect = 1.7
Identities = 16/47 (34%), Positives = 19/47 (40%), Gaps = 19/47 (40%)
Query: 58 IHALKQAKSANIDRVCIKSDSQFMIKCVQEWMPKWQSNGWRKADGKP 104
+ ALK AN+DRV I IK GW ADG+
Sbjct: 456 VWALKDPNGANLDRVQI-------IK------------GWVDADGET 483
>gnl|CDD|218788 pfam05872, DUF853, Bacterial protein of unknown function (DUF853).
This family consists of several bacterial proteins of
unknown function. BMEI1370 is thought to be an ATPase.
Length = 504
Score = 27.8 bits (62), Expect = 2.3
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 24 SAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALK 62
S G GVYF NPL++ V ++ N +Q HAL+
Sbjct: 290 SKGVGVYFVTQNPLDLPDTVLAQLGN---RVQ---HALR 322
>gnl|CDD|235880 PRK06860, PRK06860, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 309
Score = 27.6 bits (62), Expect = 2.4
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 26 GYGVYFGENNPLNVAGKVTGRVTNNNA-----EIQGAIHALKQ 63
G GVY +NPL + GR+ +N + +++G I ALK+
Sbjct: 151 GIGVYRPNDNPLYDWLQTWGRLRSNKSMLDRKDLKGMIKALKK 193
>gnl|CDD|222192 pfam13519, VWA_2, von Willebrand factor type A domain.
Length = 172
Score = 26.9 bits (60), Expect = 3.2
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 15/75 (20%)
Query: 2 DPDNHVVVFTDGACPRNG----KVGASAG---YGVYFGENNP----LNVAGKVTG----R 46
+V+ TDG + AG Y + G + L K TG
Sbjct: 98 GGSGAIVLITDGEDTPSLLEAASALKQAGVRVYVLGVGTDEGAEDALQRLAKATGGRYVD 157
Query: 47 VTNNNAEIQGAIHAL 61
T + A++ + A+
Sbjct: 158 ATADAADLDALLQAI 172
>gnl|CDD|133006 cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates
N-acetylneuraminic acid by adding CMP moiety.
CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc
synthetase) or acylneuraminate cytidylyltransferase
catalyzes the transfer the CMP moiety of CTP to the
anomeric hydroxyl group of NeuAc in the presence of
Mg++. It is the second to last step in the sialylation
of the oligosaccharide component of glycoconjugates by
providing the activated sugar-nucleotide cytidine
5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac),
the substrate for sialyltransferases. Eukaryotic
CMP-NeuAc synthetases are predominantly located in the
nucleus. The activated CMP-Neu5Ac diffuses from the
nucleus into the cytoplasm.
Length = 223
Score = 26.7 bits (60), Expect = 4.2
Identities = 5/31 (16%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 59 HALKQAKSAN-IDRVCIKSDSQFMIKCVQEW 88
++ A + DRV + +D + + + +++
Sbjct: 31 WTIEAALESKLFDRVVVSTDDEEIAEVARKY 61
>gnl|CDD|235473 PRK05450, PRK05450, 3-deoxy-manno-octulosonate
cytidylyltransferase; Provisional.
Length = 245
Score = 26.6 bits (60), Expect = 4.9
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 52 AEIQGA---IHALKQAKSANIDRVCIKSDSQ 79
A+I G + ++A A DRV + +D +
Sbjct: 22 ADIGGKPMIVRVYERASKAGADRVVVATDDE 52
>gnl|CDD|216984 pfam02348, CTP_transf_3, Cytidylyltransferase. This family
consists of two main Cytidylyltransferase activities:
1) 3-deoxy-manno-octulosonate cytidylyltransferase,,
EC:2.7.7.38 catalyzing the reaction:- CTP +
3-deoxy-D-manno-octulosonate <=> diphosphate +
CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate
cytidylyltransferase EC:2.7.7.43, catalyzing the
reaction:- CTP + N-acylneuraminate <=> diphosphate +
CMP-N-acylneuraminate. NeuAc cytydilyltransferase of
Mannheimia haemolytica has been characterized
describing kinetics and regulation by substrate charge,
energetic charge and amino-sugar demand.
Length = 197
Score = 26.5 bits (59), Expect = 5.8
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 54 IQGAIHALKQAKSANIDRVCIKSDSQFMIKCVQE 87
I I A Q S D+V + +DS+ + ++
Sbjct: 27 IARVIEAALQ--SKLFDKVVVATDSEEIADIAEK 58
>gnl|CDD|238634 cd01309, Met_dep_hydrolase_C, Metallo-dependent hydrolases,
subgroup C is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal ion
(or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown.
Length = 359
Score = 26.5 bits (59), Expect = 6.4
Identities = 16/60 (26%), Positives = 22/60 (36%), Gaps = 1/60 (1%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
VV+ TDG + + A AG + GE NP V G A +A+
Sbjct: 101 GVVIKTDGGTIEDMFIKAPAGLKMALGE-NPKRVYGGKGKEPATRMGVAALLRDAFIKAQ 159
>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in
RNA-binding protein 19 (RBM19 or RBD-1) and RNA
recognition motif 5 in multiple RNA-binding
domain-containing protein 1 (MRD1). This subfamily
corresponds to the RRM6 of RBM19 and RRM5 of MRD1.
RBM19, also termed RNA-binding domain-1 (RBD-1), is a
nucleolar protein conserved in eukaryotes. It is
involved in ribosome biogenesis by processing rRNA and
is essential for preimplantation development. It has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). MRD1 is
encoded by a novel yeast gene MRD1 (multiple RNA-binding
domain). It is well-conserved in yeast and its homologs
exist in all eukaryotes. MRD1 is present in the
nucleolus and the nucleoplasm. It interacts with the 35
S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs
(snoRNAs). It is essential for the initial processing at
the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1
contains 5 conserved RRMs, which may play an important
structural role in organizing specific rRNA processing
events. .
Length = 76
Score = 24.9 bits (55), Expect = 7.5
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 107 NKEELQELLHQIGQMESVK 125
K+EL+EL GQ++SV+
Sbjct: 13 TKKELRELFSPFGQVKSVR 31
>gnl|CDD|233778 TIGR02207, lipid_A_htrB, lipid A biosynthesis lauroyl (or
palmitoleoyl) acyltransferase. This model represents a
narrow clade of acyltransferases, nearly all of which
transfer a lauroyl group to KDO2-lipid IV-A, a lipid A
precursor; these proteins are termed lipid A
biosynthesis lauroyl acyltransferase, HtrB. An exception
is a closely related paralog of E. coli HtrB, LpxP,
which acts in cold shock conditions by transferring a
palmitoleoyl rather than lauroyl group to the lipid A
precursor. Members of this family are homologous to the
family of acyltransferases responsible for the next step
in lipid A biosynthesis [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 303
Score = 26.1 bits (58), Expect = 7.6
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 26 GYGVYFGENNPLNVAGKVTGRVTNNNA-----EIQGAIHALKQ 63
G GVY NNPL + GR+ +N A +++G I ALK
Sbjct: 145 GIGVYRPHNNPLFDWIQTRGRLRSNKAMIDRKDLRGMIKALKN 187
>gnl|CDD|233279 TIGR01125, TIGR01125, ribosomal protein S12 methylthiotransferase
RimO. Members of this protein are the
methylthiotransferase RimO, which modifies a conserved
Asp residue in ribosomal protein S12. This clade of
radical SAM family proteins is closely related to the
tRNA modification bifunctional enzyme MiaB (see
TIGR01574), and it catalyzes the same two types of
reactions: a radical-mechanism sulfur insertion, and a
methylation of the inserted sulfur. This clade spans
alpha and gamma proteobacteria, cyano bacteria,
Deinococcus, Porphyromonas, Aquifex, Helicobacter,
Campylobacter, Thermotoga, Chlamydia, Streptococcus
coelicolor and Clostridium, but does not include most
other gram positive bacteria, archaea or eukaryotes
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 430
Score = 26.2 bits (58), Expect = 8.0
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 102 GKPVQNKEELQELLHQIGQMESVKW 126
GK + + +L +LL ++G++ + W
Sbjct: 195 GKDLYRESKLVDLLEELGKVGGIYW 219
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
0.315 0.131 0.414
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,576,800
Number of extensions: 640178
Number of successful extensions: 542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 521
Number of HSP's successfully gapped: 35
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.6 bits)