RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10810
(786 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 = 118 bits (299), Expect = 2e-31
Identities = 48/125 (38%), Positives = 65/125 (52%), Gaps = 6/125 (4%)
Query: 518 IYTDGSKNEQGVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKELG--ACK 574
IYTDGSK E G I K R + L S+F AEL A+L++L G A K
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 575 ALIITDSLSCLQAITNMFHENPLVKRVQ---EELSSIEPSIEFLWCPSHVGIAGNEAADE 631
I +DS + L+A+ + +PLV R++ EL++ + W P H GI GNE AD
Sbjct: 62 ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
Query: 632 EAKQA 636
AK+A
Sbjct: 122 LAKEA 126
>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 = 82.7 bits (205), Expect = 8e-19
Identities = 41/130 (31%), Positives = 56/130 (43%), Gaps = 14/130 (10%)
Query: 515 HIKIYTDGS--KNEQGVGCALTIP-EKNIAKRFGLNKNASIFHAELFALLQSLLTIKELG 571
+ +YTDGS N G K +K + AEL AL+++L + L
Sbjct: 3 AVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLP---GTTNQRAELLALIEAL---EALS 56
Query: 572 ACKALIITDSLSCLQAITNMF---HE-NPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNE 627
K I TDS + ITN + E P+ + E L + + W P H GI GNE
Sbjct: 57 GQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQK-KHKVYIQWVPGHSGIPGNE 115
Query: 628 AADEEAKQAI 637
AD+ AKQ
Sbjct: 116 LADKLAKQGA 125
>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 = 80.4 bits (199), Expect = 5e-17
Identities = 34/123 (27%), Positives = 65/123 (52%), Gaps = 17/123 (13%)
Query: 170 GIPQGGVVSGTLFAIAINSITSYI---------HPSLSSSLFVDDFAIFTRDKNKEVLVS 220
G+ QG +S LF +A++ + + P ++ + DD +F+ K+++
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRK---- 161
Query: 221 IMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLG 280
+QE + +L+ +S ++GL +P KS+ +L K K ++ + T IE V+TFK+LG
Sbjct: 162 -LQELLQRLQEWSKESGLKINPSKSKVMLIGNKKK---RLKDITLNGTPIEAVETFKYLG 217
Query: 281 LTF 283
+T
Sbjct: 218 VTI 220
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 72.0 bits (177), Expect = 8e-15
Identities = 39/148 (26%), Positives = 60/148 (40%), Gaps = 26/148 (17%)
Query: 514 SHIKIYTDG-SKNEQGV-GCA----LTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTI 567
++I+TDG G G EK ++ G N AEL AL+++L +
Sbjct: 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR---AELRALIEALEAL 58
Query: 568 KELGACKALIITDSLSCLQAITNMFHENP----------------LVKRVQEELSSIEPS 611
KELGAC+ + TDS ++ IT + L + + E L
Sbjct: 59 KELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRH-EL 117
Query: 612 IEFLWCPSHVGIAGNEAADEEAKQAINN 639
+ + W H G NE AD+ A++A
Sbjct: 118 VFWEWVKGHAGHPENERADQLAREAARA 145
>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 = 61.2 bits (149), Expect = 3e-11
Identities = 38/127 (29%), Positives = 51/127 (40%), Gaps = 12/127 (9%)
Query: 519 YTDGSKNEQG--VGCALTIPEKNIAKRFGL---NKNASIFHAELFALLQSLLTIKELGAC 573
TDGS G + + A F A+ AEL ALL++L +LG
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 574 KALIITDSLSCLQAITN---MFHENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAAD 630
K +I TDS + I + + +N L+ L S I F P GNE AD
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116
Query: 631 EEAKQAI 637
AK+A
Sbjct: 117 RLAKEAA 123
>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 = 59.4 bits (145), Expect = 2e-10
Identities = 38/142 (26%), Positives = 57/142 (40%), Gaps = 23/142 (16%)
Query: 516 IKIYTDGS-KNEQGVG--CALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGA 572
I IYTDG+ G G A+ + + G + EL A++++L +KE
Sbjct: 2 ITIYTDGACLGNPGPGGWAAILRYGDHEKELSGGEAGTTNNRMELTAVIEALEALKE--P 59
Query: 573 CKALIITDSLSCLQAITNMFH---------------ENP-LVKRVQEELSSIEPSIEFLW 616
C L+ TDS + IT H +N L + + L+ + + W
Sbjct: 60 CPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQELDALLAK--HQVTWHW 117
Query: 617 CPSHVGIAGNEAADEEAKQAIN 638
H G GNE ADE A A +
Sbjct: 118 VKGHAGHPGNERADELANAAAD 139
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 54.3 bits (131), Expect = 3e-08
Identities = 28/129 (21%), Positives = 50/129 (38%), Gaps = 32/129 (24%)
Query: 158 IDTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYI---HPSLSSSLFVDDFAIFTRDKN 214
++ G+PQG V+S LF + +N + + P L+ + DD IF++
Sbjct: 95 VNGNPGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDILIFSKSP- 153
Query: 215 KEVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVD 274
+QE ++++ F + GL +P+K++ I D
Sbjct: 154 -----EELQEILEEVLEFLKELGLKLNPEKTK-----------------------ITHSD 185
Query: 275 TFKFLGLTF 283
KFLG
Sbjct: 186 EVKFLGYVI 194
Score = 43.9 bits (104), Expect = 1e-04
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 7/87 (8%)
Query: 73 IFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYI---HPSL 129
+++ R+F + +N + G+PQG V+S LF + +N + + P L
Sbjct: 80 GLPQRFIRWRTFSVLVNGN--PGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGL 137
Query: 130 SSSLFVDDFAIFTRDKNKEVLVSIMQE 156
+ + DD IF+ K+ E L I++E
Sbjct: 138 TYLRYADDILIFS--KSPEELQEILEE 162
>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 = 46.1 bits (110), Expect = 5e-06
Identities = 34/139 (24%), Positives = 58/139 (41%), Gaps = 26/139 (18%)
Query: 518 IYTDGSKNEQGVGCA-LTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKAL 576
++TDGS + G A +T P+ +A AEL AL+++L K K +
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQ--RAELIALIRALELAKG----KPV 55
Query: 577 -IITDSL---SCLQAITNMFHENPLVKR----VQEELSSIEPSIE------FLWCPSHVG 622
I TDS L A+ ++ E + + + ++ +I+ + +H G
Sbjct: 56 NIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSG 115
Query: 623 -----IAGNEAADEEAKQA 636
GN AD+ A+QA
Sbjct: 116 LPGPLALGNARADQAARQA 134
>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 = 46.4 bits (111), Expect = 6e-06
Identities = 32/104 (30%), Positives = 46/104 (44%), Gaps = 21/104 (20%)
Query: 555 AELFALLQSLLTIKELGA--CKALIITDSLSCLQAITNMFH---------------EN-P 596
AEL A++ +L IKE+G K +I TDS + +T N
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 597 LVKRVQEELSSIEP---SIEFLWCPSHVGIAGNEAADEEAKQAI 637
L+K + + L +E ++F P H GI GNE AD AK+
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGA 149
>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 = 41.8 bits (99), Expect = 7e-05
Identities = 26/93 (27%), Positives = 40/93 (43%), Gaps = 9/93 (9%)
Query: 551 SIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITN--MFHEN--PLVKRVQEELS 606
S AE ALL+ L ELG + ++ +DS +Q I L++ +++ L
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK 60
Query: 607 SIEPSIEFLWCPSHVGIAGNEAADEEAKQAINN 639
+ S+ SHV N AD AK A +
Sbjct: 61 KFD-SVSV----SHVPRECNRVADALAKLASAS 88
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 42.9 bits (102), Expect = 1e-04
Identities = 39/147 (26%), Positives = 60/147 (40%), Gaps = 25/147 (17%)
Query: 513 QSHIKIYTDGS-KNEQGVG--CALTI---PEKNIAKRFGLNKNASIFHAELFALLQSLLT 566
++IYTDG+ G G A+ EK ++ L N + EL A +++L
Sbjct: 1 MKQVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRM---ELMAAIEALEA 57
Query: 567 IKELGACKALIITDSLSCLQAITNMFH----------ENPLVKRV---QEELSSIEP-SI 612
+KE C+ + TDS Q IT H + VK V Q ++++ I
Sbjct: 58 LKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQI 115
Query: 613 EFLWCPSHVGIAGNEAADEEAKQAINN 639
++ W H G NE DE A+
Sbjct: 116 KWHWVKGHAGHPENERCDELARAGAEE 142
>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 = 41.0 bits (97), Expect = 3e-04
Identities = 34/136 (25%), Positives = 50/136 (36%), Gaps = 23/136 (16%)
Query: 516 IKIYTDGSKNEQ----GVGCALTIPEKNIAKR-FGLNKNASIFHAELFALLQSLLTIKEL 570
+Y DG+ G G + P+ + ++ L A+ AE AL+ L EL
Sbjct: 1 WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALEL 60
Query: 571 GACKALIITDSLSCLQAITNMFHEN---------PLVKRVQEELSSIEPSIEFLWCPSHV 621
G K I DS Q + N P ++ +E L +E W P
Sbjct: 61 GIKKLEIYGDS----QLVVNQIQGEYEVKNERLAPYLEEARELLKKF-EEVEIKWIPRE- 114
Query: 622 GIAGNEAADEEAKQAI 637
N+ AD A QA+
Sbjct: 115 ---ENKEADALANQAL 127
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III
(ExoIII) and Neisseria meningitides NExo-like subfamily
of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Escherichia
coli ExoIII, Neisseria meningitides NExo,and related
proteins. These are ExoIII family AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiencies. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity. For example, Neisseria meningitides Nape and
NExo, and exonuclease III (ExoIII) and endonuclease IV
(EndoIV) in Escherichia coli. NExo and ExoIII are
found in this subfamily. NExo is the non-dominant AP
endonuclease. It exhibits strong 3'-5' exonuclease and
3'-deoxyribose phosphodiesterase activities.
Escherichia coli ExoIII is an active AP endonuclease,
and in addition, it exhibits double strand
(ds)-specific 3'-5' exonuclease, exonucleolytic RNase
H, 3'-phosphomonoesterase and 3'-phosphodiesterase
activities, all catalyzed by a single active site.
Class II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes ExoIII and
endonuclease IV (EndoIV). This subfamily belongs to the
ExoIII family; the EndoIV family belongs to a different
superfamily.
Length = 254
Score = 42.5 bits (101), Expect = 5e-04
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 4 ILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLK-EEENFTLKGFNTVGTYEVILRQL 62
I WNVN ++ L + L++ +P ++C+QE K E++ F F +G Y V +
Sbjct: 3 IATWNVNSIRARLEQVLDWLKEEDPDVLCLQE--TKVEDDQFPADAFEALG-YHVAVHGQ 59
Query: 63 HKWN 66
+N
Sbjct: 60 KAYN 63
>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 = 39.0 bits (92), Expect = 0.002
Identities = 28/141 (19%), Positives = 53/141 (37%), Gaps = 27/141 (19%)
Query: 516 IKIYTDGSKNEQ----GVGCALTIPEKNIAKRFGLNKNASIFH----AELFALLQSLLTI 567
+ Y DGS N++ G G + + I N E+ ++++
Sbjct: 1 VIAYVDGSYNKETKVYGYGVVILKNGEEIKFSGSGNDPELASMRNVAGEIKGAIKAMEYA 60
Query: 568 KELGACKALII-----------TDSLSCLQAITNMFHENPLVKRVQEELSSIEPSIEFLW 616
E G K + I T + T + E + ++++++ I F+
Sbjct: 61 VENGI-KKITIYYDYEGIEKWATGEWKANKEGTKEYKE--FMDKIKKKIK-----ISFVK 112
Query: 617 CPSHVGIAGNEAADEEAKQAI 637
+H G NE AD+ AK+A+
Sbjct: 113 VKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the
ExoIII family purinic/apyrimidinic (AP) endonucleases.
This subfamily includes human Ape1 (also known as Apex,
Hap1, or Ref-1) and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity; for example, Ape1 and Ape2 in humans. Ape1 is
found in this subfamily, it exhibits strong
AP-endonuclease activity but shows weak 3'-5'
exonuclease and 3'-phosphodiesterase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes exonuclease
III (ExoIII) and endonuclease IV (EndoIV). This
subfamily belongs to the ExoIII family; the EndoIV
family belongs to a different superfamily.
Length = 253
Score = 40.2 bits (95), Expect = 0.002
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 12/58 (20%)
Query: 4 ILQWNVNG----VKNHLNDLTIKLRDINPKIICIQE-----SHLKEEENFTLKGFNTV 52
I+ WNVNG +K L D ++ +P I+C+QE + +E LKG++
Sbjct: 3 IISWNVNGLRALLKKGLLDY---VKKEDPDILCLQETKLQEGDVPKELKELLKGYHQY 57
>gnl|CDD|197311 cd09077, R1-I-EN, Endonuclease domain encoded by various R1- and
I-clade non-long terminal repeat retrotransposons.
This family contains the endonuclease (EN) domain of
various non-long terminal repeat (non-LTR)
retrotransposons, long interspersed nuclear elements
(LINEs) which belong to the subtype 2, R1- and I-clade.
LINES can be classified into two subtypes. Subtype 2
has two ORFs: the second (ORF2) encodes a modular
protein consisting of an N-terminal apurine/apyrimidine
endonuclease domain (EN), a central reverse
transcriptase, and a zinc-finger-like domain at the
C-terminus. Most non-LTR retrotransposons are inserted
throughout the host genome; however, many
retrotransposons of the R1 clade exhibit
target-specific retrotransposition. This family
includes the endonucleases of SART1 and R1bm, from the
silkworm Bombyx mori, which belong to the R1-clade. It
also includes the endonuclease of snail (Biomphalaria
glabrata) Nimbus/Bgl and mosquito Aedes aegypti
(MosquI), both which belong to the I-clade. This family
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 205
Score = 39.6 bits (93), Expect = 0.003
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 2 VNILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLKEEEN 43
+ ILQ N+N K + L R+ I IQE +L N
Sbjct: 1 LRILQINLNRCKAAQDLLLQTAREEGADIALIQEPYLVPVNN 42
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination,
and repair].
Length = 261
Score = 38.0 bits (89), Expect = 0.012
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 4 ILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLK-EEENFTLKGFNTVGTYEVI 58
I WNVNG++ L L L + P ++C+QE K ++E F + +G + V
Sbjct: 3 IASWNVNGLRARLKKLLDWLEEEQPDVLCLQE--TKAQDEQFPREELEALGYHHVF 56
>gnl|CDD|238826 cd01648, TERT, TERT: Telomerase reverse transcriptase (TERT).
Telomerase is a ribonucleoprotein (RNP) that synthesizes
telomeric DNA repeats. The telomerase RNA subunit
provides the template for synthesis of these repeats.
The catalytic subunit of RNP is known as telomerase
reverse transcriptase (TERT). The reverse transcriptase
(RT) domain is located in the C-terminal region of the
TERT polypeptide. Single amino acid substitutions in
this region lead to telomere shortening and senescence.
Telomerase is an enzyme that, in certain cells,
maintains the physical ends of chromosomes (telomeres)
during replication. In somatic cells, replication of the
lagging strand requires the continual presence of an RNA
primer approximately 200 nucleotides upstream, which is
complementary to the template strand. Since there is a
region of DNA less than 200 base pairs from the end of
the chromosome where this is not possible, the
chromosome is continually shortened. However, a surplus
of repetitive DNA at the chromosome ends protects
against the erosion of gene-encoding DNA. Telomerase is
not normally expressed in somatic cells. It has been
suggested that exogenous TERT may extend the lifespan
of, or even immortalize, the cell. However, recent
studies have shown that telomerase activity can be
induced by a number of oncogenes. Conversely, the
oncogene c-myc can be activated in human TERT
immortalized cells. Sequence comparisons place the
telomerase proteins in the RT family but reveal
hallmarks that distinguish them from retroviral and
retrotransposon relatives.
Length = 119
Score = 33.8 bits (78), Expect = 0.078
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 16/97 (16%)
Query: 159 DTLSEDFSIVCGIPQGGVVSGTLFAIAINSI----TSYIHPSLSSSL---FVDDFAIFT- 210
D++ + + GIPQG +S L ++ + S++ SL VDDF + T
Sbjct: 8 DSIPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITT 67
Query: 211 -RDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQ 246
DK + L +++ F N F + K+Q
Sbjct: 68 SLDKAIKFL-NLLLRG------FINQYKTFVNFDKTQ 97
Score = 30.3 bits (69), Expect = 1.3
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 97 FSIVCGIPQGGVVSGTLFAIAINSI----TSYIHPSLSSSL---FVDDFAIFTRDKNK 147
+ GIPQG +S L ++ + S++ SL VDDF + T +K
Sbjct: 14 YRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLDK 71
>gnl|CDD|238824 cd01646, RT_Bac_retron_I, RT_Bac_retron_I: Reverse transcriptases
(RTs) in bacterial retrotransposons or retrons. The
polymerase reaction of this enzyme leads to the
production of a unique RNA-DNA complex called msDNA
(multicopy single-stranded (ss)DNA) in which a small
ssDNA branches out from a small ssRNA molecule via a
2'-5'phosphodiester linkage. Bacterial retron RTs
produce cDNA corresponding to only a small portion of
the retron genome.
Length = 158
Score = 34.6 bits (80), Expect = 0.080
Identities = 26/136 (19%), Positives = 49/136 (36%), Gaps = 14/136 (10%)
Query: 126 HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSEDFSIVCGIPQGGVVSGTLFA-I 184
SL +L A + + + + + S+ G+P G + S A I
Sbjct: 12 THSLPWALHGKIKAKQLLKLLRLLGNLL--DLLLLSSQYGQTN-GLPIGPLTSR-FLANI 67
Query: 185 AINSITSYIHPSLSSSL---FVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFS 241
+N + + L +VDD IF +KE I+ ++L+ F + GL +
Sbjct: 68 YLNDVDHELKSKLKGVDYVRYVDDIRIFA--DSKEEAEEIL----EELKEFLAELGLSLN 121
Query: 242 PQKSQCVLFSRKYKQL 257
K++ +
Sbjct: 122 LSKTEILPLPEGTASK 137
Score = 34.2 bits (79), Expect = 0.10
Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 7/88 (7%)
Query: 80 DPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFA-IAINSITSYIHPSLSSSL---FV 135
R L+ +LS + G+P G + S A I +N + + L +V
Sbjct: 31 LLRLLGNLLDLLLLSSQYGQTNGLPIGPLTSR-FLANIYLNDVDHELKSKLKGVDYVRYV 89
Query: 136 DDFAIFTRDKNKEVLVSIMQESIDTLSE 163
DD IF +KE I++E + L+E
Sbjct: 90 DDIRIFA--DSKEEAEEILEELKEFLAE 115
>gnl|CDD|187699 cd09275, RNase_HI_RT_DIRS1, DIRS1 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 eukaryotes. 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. The structural features of DIRS1-group
elements are different from typical LTR elements. RNase
H inhibitors have been explored as an anti-HIV drug
target because RNase H inactivation inhibits reverse
transcription.
Length = 120
Score = 33.8 bits (78), Expect = 0.097
Identities = 22/101 (21%), Positives = 34/101 (33%), Gaps = 26/101 (25%)
Query: 549 NASIFHAELFALLQSLLTI-KELGACKALIITDSLSCLQAITNM-----FHENPLVKRVQ 602
N I EL A+L +L L K L+ +D+ + + I L +++
Sbjct: 30 NKHINFLELLAVLLALQHWGARLSNRKVLVRSDNTTAVAYINRQGGTRSPELLALARQL- 88
Query: 603 EELSSIEPSIEFLWCPSH------VGIAG--NEAADEEAKQ 635
LWC I G N AAD ++
Sbjct: 89 -----------VLWCEERNIWLRARHIPGVLNVAADRLSRL 118
>gnl|CDD|197318 cd09084, EEP-2, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily; uncharacterized family 2. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of
a diverse set of proteins including the ExoIII family
of apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain
of the non-LTR retrotransposon LINE-1, and related
domains. These diverse enzymes share a common catalytic
mechanism of cleaving phosphodiester bonds; their
substrates range from nucleic acids to phospholipids
and perhaps, proteins.
Length = 246
Score = 34.2 bits (79), Expect = 0.18
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 8/79 (10%)
Query: 3 NILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLKEEENFTLKGFNTVG---TYEVIL 59
N+ +N K+ + + ++ +P I+C+QE + E + G Y V
Sbjct: 5 NVRSFNRYKWKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYPYYYVVYK 64
Query: 60 RQLHKWNMRGHLPIFLSKY 78
+ SKY
Sbjct: 65 SDSGGTGL-----AIFSKY 78
>gnl|CDD|238828 cd01651, RT_G2_intron, RT_G2_intron: Reverse transcriptases (RTs)
with group II intron origin. RT transcribes DNA using
RNA as template. Proteins in this subfamily are found in
bacterial and mitochondrial group II introns. Their most
probable ancestor was a retrotransposable element with
both gag-like and pol-like genes. This subfamily of
proteins appears to have captured the RT sequences from
transposable elements, which lack long terminal repeats
(LTRs).
Length = 226
Score = 34.1 bits (79), Expect = 0.20
Identities = 30/130 (23%), Positives = 41/130 (31%), Gaps = 45/130 (34%)
Query: 170 GIPQGGVVSGTLFAIA-----------INSITSYIHPSLSSSLFV---DDFAIFTRDKNK 215
G PQGGV+S L I + P +V DDF I R +
Sbjct: 126 GTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKE 185
Query: 216 EVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIE--VV 273
+ + + F + GL +P+K TRI
Sbjct: 186 AEEI------KELIREFLEELGLELNPEK-----------------------TRITHFKS 216
Query: 274 DTFKFLGLTF 283
+ F FLG TF
Sbjct: 217 EGFDFLGFTF 226
>gnl|CDD|188032 TIGR00195, exoDNase_III, exodeoxyribonuclease III. The model
brings in reverse transcriptases at scores below 50,
model also contains eukaryotic apurinic/apyrimidinic
endonucleases which group in the same family [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 254
Score = 33.9 bits (78), Expect = 0.25
Identities = 16/55 (29%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 4 ILQWNVNGVKNHLNDLTIKLRDINPKIICIQESHLKEEENFTLKGFNTVGTYEVI 58
I+ WNVNG++ + L++ P ++C+QE+ + ++E F L+ F+ G +
Sbjct: 3 IISWNVNGLRARPHKGLAWLKENQPDVLCLQETKV-QDEQFPLEPFHKEGYHVFF 56
>gnl|CDD|139971 PRK13911, PRK13911, exodeoxyribonuclease III; Provisional.
Length = 250
Score = 33.5 bits (76), Expect = 0.29
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 2/50 (4%)
Query: 2 VNILQWNVNGVKNHLNDLTIKL-RDINPKIICIQESHLKEEEN-FTLKGF 49
+ ++ WNVNG++ + + ++ + CIQES +++E+N F KG+
Sbjct: 1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGY 50
>gnl|CDD|197310 cd09076, L1-EN, Endonuclease domain (L1-EN) of the non-LTR
retrotransposon LINE-1 (L1), and related domains. This
family contains the endonuclease domain (L1-EN) of the
non-LTR retrotransposon LINE-1 (L1), and related
domains, including the endonuclease of Xenopus laevis
Tx1. These retrotranspons belong to the subtype 2,
L1-clade. LINES can be classified into two subtypes.
Subtype 2 has two ORFs: the second (ORF2) encodes a
modular protein consisting of an N-terminal
apurine/apyrimidine endonuclease domain (EN), a central
reverse transcriptase, and a zinc-finger-like domain at
the C-terminus. LINE-1/L1 elements (full length and
truncated) comprise about 17% of the human genome. This
endonuclease nicks the genomic DNA at the consensus
target sequence 5'TTTT-AA3' producing a ribose
3'-hydroxyl end as a primer for reverse transcription
of associated template RNA. This subgroup also includes
the endonuclease of Xenopus laevis Tx1, another member
of the L1-clade. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 236
Score = 33.5 bits (77), Expect = 0.30
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 7 WNVNGVKN--HLNDLTIKLRDINPKIICIQESHLKEEENFTLK 47
NV G+++ L +L+ I+ +QE+H E K
Sbjct: 4 LNVRGLRSPGKRAQLLEELKRKKLDILGLQETHWTGEGELKKK 46
>gnl|CDD|215242 PLN02441, PLN02441, cytokinin dehydrogenase.
Length = 525
Score = 33.3 bits (77), Expect = 0.57
Identities = 21/54 (38%), Positives = 26/54 (48%), Gaps = 12/54 (22%)
Query: 201 LFVDDFAIFTRDKNKEVLVSIMQE-SIDKLENF--SNDTGL-------FFSPQK 244
+ DF+ FTRD +E L+S E S D +E F N GL FFSP
Sbjct: 250 VLYSDFSTFTRD--QERLISRPPENSFDYVEGFVIVNRNGLINNWRSSFFSPSD 301
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III
(ExoIII)-like apurinic/apyrimidinic (AP) endonucleases.
The ExoIII family AP endonucleases belong to the large
EEP (exonuclease/endonuclease/phosphatase) superfamily
that contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, which is
then followed by the coordinated actions of DNA
polymerase, deoxyribose phosphatase, and DNA ligase. If
left unrepaired, AP sites block DNA replication, which
have both mutagenic and cytotoxic effects. AP
endonucleases can carry out a wide range of excision
and incision reactions on DNA, including 3'-5'
exonuclease, 3'-deoxyribose phosphodiesterase,
3'-phosphatase, and occasionally, nonspecific DNase
activities. Different AP endonuclease enzymes catalyze
the different reactions with different efficiences.
Many organisms have two functional AP endonucleases,
for example, APE1/Ref-1 and Ape2 in humans, Apn1 and
Apn2 in bakers yeast, Nape and NExo in Neisseria
meningitides, and exonuclease III (ExoIII) and
endonuclease IV (EndoIV) in Escherichia coli. Usually,
one of the two is the dominant AP endonuclease, the
other has weak AP endonuclease activity, but exhibits
strong 3'-5' exonuclease, 3'-deoxyribose
phosphodiesterase, and 3'-phosphatase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes. This family
contains the ExoIII family; the EndoIV family belongs
to a different superfamily.
Length = 251
Score = 32.6 bits (75), Expect = 0.60
Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 4 ILQWNVNGVKNHLNDLTIK-LRDINPKIICIQESHLKEEE 42
I+ WNVNG++ L +K L++ P I+C+QE+ E++
Sbjct: 2 IISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDK 41
>gnl|CDD|197319 cd09085, Mth212-like_AP-endo, Methanothermobacter
thermautotrophicus Mth212-like subfamily of the ExoIII
family purinic/apyrimidinic (AP) endonucleases. This
subfamily includes the thermophilic archaeon
Methanothermobacter thermautotrophicus Mth212and
related proteins. These are Escherichia coli
exonuclease III (ExoIII)-like AP endonucleases and they
belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Mth212 is an AP
endonuclease, and a DNA uridine endonuclease (U-endo)
that nicks double-stranded DNA at the 5'-side of a
2'-d-uridine residue. After incision at the 5'-side of
a 2'-d-uridine residue by Mth212, DNA polymerase B
takes over the 3'-OH terminus and carries out repair
synthesis, generating a 5'-flap structure that is
resolved by a 5'-flap endonuclease. Finally, DNA ligase
seals the resulting nick. This U-endo activity shares
the same catalytic center as its AP-endo activity, and
is absent from other AP endonuclease homologues.
Length = 252
Score = 32.2 bits (74), Expect = 0.70
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 17/71 (23%)
Query: 2 VNILQWNVNGVKN-HLNDLTIKLRDINPKIICIQESH---------LKEEENFTL----- 46
+ I+ WNVNG++ H ++ P I+C+QE+ L+ E +
Sbjct: 1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSA 60
Query: 47 --KGFNTVGTY 55
KG++ V Y
Sbjct: 61 ERKGYSGVALY 71
>gnl|CDD|233064 TIGR00633, xth, exodeoxyribonuclease III (xth). All proteins in
this family for which functions are known are 5' AP
endonucleases that funciton in base excision repair and
the repair of abasic sites in DNA.This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 255
Score = 32.3 bits (74), Expect = 0.89
Identities = 14/39 (35%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 4 ILQWNVNGVKNHLNDLTIK-LRDINPKIICIQESHLKEE 41
I+ WNVNG++ L+ L + L++ P ++C+QE+ + +E
Sbjct: 3 IISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADE 41
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily. This large superfamily includes the
catalytic domain (exonuclease/endonuclease/phosphatase
or EEP domain) of a diverse set of proteins including
the ExoIII family of apurinic/apyrimidinic (AP)
endonucleases, inositol polyphosphate 5-phosphatases
(INPP5), neutral sphingomyelinases (nSMases),
deadenylases (such as the vertebrate circadian-clock
regulated nocturnin), bacterial cytolethal distending
toxin B (CdtB), deoxyribonuclease 1 (DNase1), the
endonuclease domain of the non-LTR retrotransposon
LINE-1, and related domains. These diverse enzymes
share a common catalytic mechanism of cleaving
phosphodiester bonds; their substrates range from
nucleic acids to phospholipids and perhaps proteins.
Length = 241
Score = 31.3 bits (71), Expect = 1.5
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 4 ILQWNVNG--VKNHLNDLTIKLRDINPKIICIQESHL 38
+ +NVNG + + +R+++P I+C+QE
Sbjct: 1 VASYNVNGLNAATRASGIARWVRELDPDIVCLQEVKD 37
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 30.2 bits (67), Expect = 2.5
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 15/99 (15%)
Query: 555 AELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFHE-----------NPLVKR--V 601
AEL A+ + L+ + LI++DS + ++T + P++ + +
Sbjct: 45 AELTAVRELLIATRHTDR-PILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEII 103
Query: 602 QEELSSIEP-SIEFLWCPSHVGIAGNEAADEEAKQAINN 639
QE S +E +I W +H G NEAAD A+QA NN
Sbjct: 104 QEIDSLMENRNIRMSWVNAHTGHPLNEAADSLARQAANN 142
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
family. This large family of proteins includes
magnesium dependent endonucleases and a large number of
phosphatases involved in intracellular signalling. This
family includes: AP endonuclease proteins EC:4.2.99.18,
DNase I proteins EC:3.1.21.1, Synaptojanin an
inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
Sphingomyelinase EC:3.1.4.12 and Nocturnin.
Length = 143
Score = 29.9 bits (67), Expect = 2.6
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 5 LQWNVNGVKNHLNDLTIKLRDINPKIICIQ 34
L WNVNG+ N L L LR +P ++ +Q
Sbjct: 1 LTWNVNGLGNGLAALADLLRAQDPDVLALQ 30
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 29.8 bits (67), Expect = 3.0
Identities = 37/152 (24%), Positives = 61/152 (40%), Gaps = 37/152 (24%)
Query: 513 QSHIKIYTDGSKNEQGVGC-----ALTIPEKN--IAKRFGLNKNASIFHA--ELFALLQS 563
++ IY DG+ GC L + ++ I + N +A EL AL+++
Sbjct: 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEA 61
Query: 564 LLTIKELGACKALIITDSLSCLQAITNMFHE---------------NPLVKR----VQEE 604
L ++ +I +DS C++ F+E P+ R +E
Sbjct: 62 LEYARD----GDVIYSDSDYCVRG----FNEWLDTWKQKGWRKSDKKPVANRDLWQQVDE 113
Query: 605 LSSIEPSIEFLWCPSHVGIAGNEAADEEAKQA 636
L + +E +H GI GNEAAD A+ A
Sbjct: 114 LRA-RKYVEVEKVTAHSGIEGNEAADMLAQAA 144
>gnl|CDD|211621 TIGR01039, atpD, ATP synthase, F1 beta subunit. The sequences of
ATP synthase F1 alpha and beta subunits are related and
both contain a nucleotide-binding site for ATP and ADP.
They have a common amino terminal domain but vary at the
C-terminus. The beta chain has catalytic activity, while
the alpha chain is a regulatory subunit. Proton
translocating ATP synthase, F1 beta subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), A subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 461
Score = 30.8 bits (70), Expect = 3.1
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 681 WNKMKRNGPNEFTLQLRPQTNEVCLMRMRVGHSKLTHSHLFRRED 725
+++MK +G + T + Q NE RMRV + LT + FR E
Sbjct: 191 YHEMKESGVIDKTALVYGQMNEPPGARMRVALTGLTMAEYFRDEQ 235
>gnl|CDD|197322 cd09088, Ape2-like_AP-endo, Human Ape2-like subfamily of the
ExoIII family purinic/apyrimidinic (AP) endonucleases.
This subfamily includes human APE2, Saccharomyces
cerevisiae Apn2/Eth1, and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity. For examples, Ape1 and Ape2 in humans, and
Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are
both found in this subfamily, and have the weaker AP
endonuclease activity. Ape2 shows strong 3'-5'
exonuclease and 3'-phosphodiesterase activities; it can
reduce the mutagenic consequences of attack by reactive
oxygen species by removing 3'-end adenine opposite from
8-oxoG, in addition to repairing 3'-damaged termini.
Apn2/Eth1 exhibits AP endonuclease activity, but has
30-40 fold more active 3'-phosphodiesterase and 3'-5'
exonuclease activities. Class II AP endonucleases have
been classified into two families, designated ExoIII
and EndoIV, based on their homology to the Escherichia
coli enzymes exonuclease III (ExoIII) and endonuclease
IV (EndoIV). This subfamily belongs to the ExoIII
family; the EndoIV family belongs to a different
superfamily.
Length = 309
Score = 30.7 bits (70), Expect = 3.1
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 4 ILQWNVNGVKNHLNDL------TIK--LRDINPKIICIQE 35
I+ WNVNG++ L ++K L ++ IIC+QE
Sbjct: 2 IVTWNVNGIRTRLQYQPWNKENSLKSFLDSLDADIICLQE 41
>gnl|CDD|181088 PRK07708, PRK07708, hypothetical protein; Validated.
Length = 219
Score = 30.0 bits (68), Expect = 3.4
Identities = 37/144 (25%), Positives = 62/144 (43%), Gaps = 29/144 (20%)
Query: 515 HIKIYTDGSKNEQ----GVGCALTIPEKNIAKRFGLNKNASIFH------AELFALLQSL 564
I +Y DG +++ G+G I K KR+ + +NA I AE AL ++
Sbjct: 73 EILVYFDGGFDKETKLAGLGIV--IYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAM 130
Query: 565 LTIKELGACKALIIT---DSLSCLQAITNMF-----HENPLVKRVQEELSS--IEPSIEF 614
++ELG K +T DS L + + H N + R++++L + P E
Sbjct: 131 QELEELGV-KHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYE- 188
Query: 615 LWCPSHVGIAGNEAADEEAKQAIN 638
+ N+ AD+ A QA+
Sbjct: 189 -----PISRKQNKEADQLATQALE 207
>gnl|CDD|132850 cd07211, Pat_PNPLA8, Patatin-like phospholipase domain containing
protein 8. PNPLA8 is a Ca-independent myocardial
phospholipase which maintains mitochondrial integrity.
PNPLA8 is also known as iPLA2-gamma. In humans, it is
predominantly expressed in heart tissue. iPLA2-gamma can
catalyze both phospholipase A1 and A2 reactions (PLA1
and PLA2 respectively). This family includes PNPLA8
(iPLA2-gamma) from Homo sapiens and iPLA2-2 from Mus
musculus.
Length = 308
Score = 29.9 bits (68), Expect = 4.6
Identities = 12/65 (18%), Positives = 29/65 (44%), Gaps = 3/65 (4%)
Query: 148 EVLVSIMQESIDTLSEDFSIVCGIPQGGVVSGTL--FAIAINSITSYIHPSLSSSLFVDD 205
E+L I + + + E F +CG+ G +++ L ++++ ++ L +F +
Sbjct: 25 EILRKIEKLTGKPIHELFDYICGVSTGAILAFLLGLKKMSLDEC-EELYRKLGKDVFSQN 83
Query: 206 FAIFT 210
I
Sbjct: 84 TYISG 88
>gnl|CDD|215787 pfam00206, Lyase_1, Lyase.
Length = 312
Score = 29.6 bits (67), Expect = 6.3
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 124 YIHPSLSSS-LFVDDFAIFTRDKNKEVLVSIMQESIDTLSE 163
+H SS+ + + EVL+ + + ID L E
Sbjct: 104 KVHTGQSSNDQVPTALRLALKLALSEVLLPALGQLIDALKE 144
>gnl|CDD|238185 cd00304, RT_like, RT_like: Reverse transcriptase (RT, RNA-dependent
DNA polymerase)_like family. An RT gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. RTs occur in a variety of mobile
elements, including retrotransposons, retroviruses,
group II introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 98
Score = 27.7 bits (62), Expect = 7.7
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 10/79 (12%)
Query: 171 IPQGGVVSGTLFAIAINSITS---YIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESID 227
+PQG +S L + + + + ++ +VDD + + + + V
Sbjct: 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAV-------KKR 64
Query: 228 KLENFSNDTGLFFSPQKSQ 246
+LE F GL S +K+Q
Sbjct: 65 ELEEFLARLGLNLSDEKTQ 83
>gnl|CDD|129854 TIGR00771, DcuC, c4-dicarboxylate anaerobic carrier family protein.
These proteins are members of the C4-dicarboxylate
Uptake C (DcuC) Family (TC 2.A.61). The only
functionally characterized member of this family is the
anaerobic C4-dicarboxylate transporter (DcuC) of
Escherichia coli. DcuC has 12 GES predicted
transmembrane regions, is induced only under anaerobic
conditions, and is not repressed by glucose. It may
therefore function as a succinate efflux system during
anaerobic glucose fermentation. However, when
overexpressed, it can replace either DcuA or DcuB in
catalyzing fumarate-succinate exchange and fumarate
uptake [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 388
Score = 29.5 bits (66), Expect = 7.9
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 10/78 (12%)
Query: 132 SLFVDDFAIFTRDKNKEVLVSIMQESIDTLSEDFSIVCGIPQGGVVSGTLFAI------A 185
+ A F R N+ V I +E + + F+ V G+ +V+ ++FA A
Sbjct: 224 PQAMLIGAEFGRIVNRISPVKITEEFFNGMGNSFANVVGL----IVAASVFAAGLKTIGA 279
Query: 186 INSITSYIHPSLSSSLFV 203
+++ S+ S ++FV
Sbjct: 280 VDAAISFAKESGLGNIFV 297
>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit beta.
A small number of taxonomically diverse prokaryotic
species have what appears to be a second ATP synthase,
in addition to the normal F1F0 ATPase in bacteria and
A1A0 ATPase in archaea. These enzymes use ion gradients
to synthesize ATP, and in principle may run in either
direction. This model represents the F1 beta subunit of
this apparent second ATP synthase.
Length = 449
Score = 29.4 bits (66), Expect = 8.6
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 681 WNKMKRNGPNEFTLQLRPQTNEVCLMRMRVGHSKLTHSHLFR 722
+ +MK G + T+ + Q NE R RVGH+ LT + FR
Sbjct: 186 YREMKEAGVLDNTVMVFGQMNEPPGARFRVGHTALTMAEYFR 227
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 0.134 0.396
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,582,645
Number of extensions: 3894508
Number of successful extensions: 3683
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3653
Number of HSP's successfully gapped: 61
Length of query: 786
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 681
Effective length of database: 6,280,432
Effective search space: 4276974192
Effective search space used: 4276974192
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: 63 (28.2 bits)