RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15121
(960 letters)
>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 = 107 bits (269), Expect = 2e-27
Identities = 49/116 (42%), Positives = 69/116 (59%)
Query: 66 STDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSD 125
TDAS GWGA++ QG+W+ +R+ HIN EL V A+ + ++N V+++SD
Sbjct: 3 FTDASLSGWGAVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKVLVRSD 62
Query: 126 NKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQ 181
N T +AYI +QGG RS LLA ++L+L + NI + IPG N AD LSR
Sbjct: 63 NTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPGVLNVAADRLSRL 118
Score = 107 bits (269), Expect = 2e-27
Identities = 49/116 (42%), Positives = 69/116 (59%)
Query: 812 STDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSD 871
TDAS GWGA++ QG+W+ +R+ HIN EL V A+ + ++N V+++SD
Sbjct: 3 FTDASLSGWGAVLSGSWAQGLWSAEERNKHINFLELLAVLLALQHWGARLSNRKVLVRSD 62
Query: 872 NKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQ 927
N T +AYI +QGG RS LLA ++L+L + NI + IPG N AD LSR
Sbjct: 63 NTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPGVLNVAADRLSRL 118
Score = 58.8 bits (143), Expect = 2e-10
Identities = 27/62 (43%), Positives = 37/62 (59%)
Query: 469 VVLQSDNKTVITYIRKQVGLRSNALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALS 528
V+++SDN T + YI +Q G RS LLA ++L+L + NI + IPG N AD LS
Sbjct: 57 VLVRSDNTTAVAYINRQGGTRSPELLALARQLVLWCEERNIWLRARHIPGVLNVAADRLS 116
Query: 529 RQ 530
R
Sbjct: 117 RL 118
>gnl|CDD|239684 cd03714, RT_DIRS1, RT_DIRS1: Reverse transcriptases (RTs) occurring
in the DIRS1 group of retransposons. Members of the
subfamily include the Dictyostelium DIRS-1, Volvox
carteri kangaroo, and Panagrellus redivivus PAT
elements. These elements differ from LTR and
conventional non-LTR retrotransposons. They contain
split direct repeat (SDR) termini, and have been
proposed to integrate via double-stranded closed-circle
DNA intermediates assisted by an encoded recombinase
which is similar to gamma-site-specific integrase.
Length = 119
Score = 78.2 bits (193), Expect = 3e-17
Identities = 40/113 (35%), Positives = 55/113 (48%), Gaps = 5/113 (4%)
Query: 355 IDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRERG 414
+DL AY HIPI R R L F ++G YQ L FGL+ AP+ F ++ + LR G
Sbjct: 1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLG 60
Query: 415 VRCLVYLDDFLLASQDSV----VLKNQIFQTLPVNLSGNCSRSGRRSHPTHSL 463
VR YLDD L+ + VL++ TL NL + + PT +
Sbjct: 61 VRIFSYLDDLLIIASSIKTSEAVLRHL-RATLLANLGFTLNLEKSKLGPTQRI 112
Score = 67.8 bits (166), Expect = 2e-13
Identities = 40/119 (33%), Positives = 58/119 (48%), Gaps = 11/119 (9%)
Query: 649 IDLSQAYCHIPIARRHRRFLCFLIPMDMSSFRPSL-----SSPGVCPTIKLG--RRLRER 701
+DL AY HIPI R R L F + +L +P V + LR
Sbjct: 1 VDLKDAYFHIPILPRSRDLLGF-AWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLL 59
Query: 702 GVRCLVYLDDFLLASQDPIVLKNQILQTL--QLLTYLGWQVNLKKSQIIPSHRVDYLGI 758
GVR YLDD L+ + I +L+ L LL LG+ +NL+KS++ P+ R+ +LG+
Sbjct: 60 GVRIFSYLDDLLIIASS-IKTSEAVLRHLRATLLANLGFTLNLEKSKLGPTQRITFLGL 117
>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 = 63.1 bits (154), Expect = 3e-11
Identities = 49/189 (25%), Positives = 81/189 (42%), Gaps = 37/189 (19%)
Query: 606 GDGTMRPV--FNLKSLNSYVTTKKFKLINHQKIPLF---------LQKNDYLATIDLSQA 654
G G RP+ + K LN T K+ + I P F L+ + + +DL +A
Sbjct: 5 GKGKYRPISSVDYKILNK-ATKKRLEPIFSPPQPGFRPGRSTHNLLKGSKWFLKLDLKKA 63
Query: 655 YCHIP---IARRHRRFLCFLIPMDMSSFRPSLS-SPGVC-------------PTI----- 692
+ IP + R F + +F ++ +PG P +
Sbjct: 64 FDSIPHDPLDRPLTAFGLPQRFIRWRTFSVLVNGNPGGRYEWRGLPQGSVLSPLLFNLFM 123
Query: 693 -KLGRRLRER--GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIP 749
+L R LR+R G+ L Y DD L+ S+ P L+ + + L+ L LG ++N +K++I
Sbjct: 124 NELLRPLRKRFPGLTYLRYADDILIFSKSPEELQEILEEVLEFLKELGLKLNPEKTKITH 183
Query: 750 SHRVDYLGI 758
S V +LG
Sbjct: 184 SDEVKFLGY 192
Score = 40.8 bits (96), Expect = 0.001
Identities = 27/128 (21%), Positives = 43/128 (33%), Gaps = 19/128 (14%)
Query: 322 LKSLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIAR------------- 368
K L + + + L+ + + +DL +A+ IP
Sbjct: 25 KKRLEPIFSPPQPGFRPGRSTHNLLKGSKWFLKLDLKKAFDSIPHDPLDRPLTAFGLPQR 84
Query: 369 ----RHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRER--GVRCLVYLD 422
R L G Y+ L G +P F N + LR+R G+ L Y D
Sbjct: 85 FIRWRTFSVLVNGNPGGRYEWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYAD 144
Query: 423 DFLLASQD 430
D L+ S+
Sbjct: 145 DILIFSKS 152
>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
retrotransposons and retroviruses which have long
terminal repeats (LTRs) in their DNA copies but not in
their RNA template. RT catalyzes DNA replication from an
RNA template, and is responsible for the replication of
retroelements. An RT gene is usually indicative of a
mobile element such as a retrotransposon or retrovirus.
RTs are present in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
Caulimoviruses.
Length = 177
Score = 60.3 bits (147), Expect = 2e-10
Identities = 28/85 (32%), Positives = 39/85 (45%), Gaps = 2/85 (2%)
Query: 346 LQKNDYLATIDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNW 405
L + +DL Y IP+A R F +Y+ T + FGL +AP F +L N
Sbjct: 54 LAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNK 113
Query: 406 VAVLLRERGVRCLVYLDDFLLASQD 430
+L G VYLDD L+ S+
Sbjct: 114 --ILGDLLGDFVEVYLDDILVYSKT 136
Score = 44.5 bits (106), Expect = 6e-05
Identities = 35/158 (22%), Positives = 60/158 (37%), Gaps = 11/158 (6%)
Query: 607 DGTMRPVFNLKSLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRR 666
DG +R + + LN ++ L ++ L + +DL Y IP+A R
Sbjct: 21 DGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRP 80
Query: 667 FLCFLIPMDMSSFRPSLSSPGVC--PTIKLGRRLR-----ERGVRCLVYLDDFLLASQDP 719
F P + + G+ P R + G VYLDD L+ S+
Sbjct: 81 KTAFRTP--FGLYEYTRMPFGLKNAPAT-FQRLMNKILGDLLGDFVEVYLDDILVYSKTE 137
Query: 720 IVLKNQILQTLQLLTYLGWQVNLKKSQIIPSHRVDYLG 757
+ + L+ L G ++N +K + V++LG
Sbjct: 138 EEHLEHLREVLERLREAGLKLNPEKCEFG-VPEVEFLG 174
>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 = 51.2 bits (123), Expect = 9e-08
Identities = 25/129 (19%), Positives = 50/129 (38%), Gaps = 19/129 (14%)
Query: 67 TDASD------VGWGAMVGNVSVQGVWTQAQRSWH--INLKELFTVRAAISSNPSLVA-- 116
TD S G G ++ + ++ + N EL + A+ +A
Sbjct: 2 TDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEAL-----ELALD 56
Query: 117 --NHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSL 174
+++++D+K V+ I L LLL+ ++I +P + N +
Sbjct: 57 LGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFE--HVPREGNEV 114
Query: 175 ADALSRQAL 183
AD L+++A
Sbjct: 115 ADRLAKEAA 123
Score = 51.2 bits (123), Expect = 9e-08
Identities = 25/129 (19%), Positives = 50/129 (38%), Gaps = 19/129 (14%)
Query: 813 TDASD------VGWGAMVGNVSVQGVWTQAQRSWH--INLKELFTVRAAISSNPSLVA-- 862
TD S G G ++ + ++ + N EL + A+ +A
Sbjct: 2 TDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEAL-----ELALD 56
Query: 863 --NHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSL 920
+++++D+K V+ I L LLL+ ++I +P + N +
Sbjct: 57 LGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFE--HVPREGNEV 114
Query: 921 ADALSRQAL 929
AD L+++A
Sbjct: 115 ADRLAKEAA 123
Score = 45.8 bits (109), Expect = 8e-06
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 466 NHTVVLQSDNKTVITYIRKQVGLRSNALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLAD 525
+++++D+K V+ I L LLL+ ++I +P + N +AD
Sbjct: 59 LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFE--HVPREGNEVAD 116
Query: 526 ALSRQAL 532
L+++A
Sbjct: 117 RLAKEAA 123
>gnl|CDD|239685 cd03715, RT_ZFREV_like, RT_ZFREV_like: A subfamily of reverse
transcriptases (RTs) found in sequences similar to the
intact endogenous retrovirus ZFERV from zebrafish and to
Moloney murine leukemia virus RT. 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. Phylogenetic analysis suggests
that ZFERV belongs to a distinct group of retroviruses.
Length = 210
Score = 47.7 bits (114), Expect = 7e-06
Identities = 42/172 (24%), Positives = 65/172 (37%), Gaps = 36/172 (20%)
Query: 611 RPVFNLKSLNSYVTTKKFKLINHQKIP-------LFLQKNDYLATIDLSQAYCHIPIARR 663
R V +L+ +N V H +P L K+ + +DL+ A+ +P+A
Sbjct: 53 RMVQDLRLVNQAVLPI------HPAVPNPYTLLSLLPPKHQWYTVLDLANAFFSLPLAPD 106
Query: 664 HRRFLCF----------LIPMDMSSFRPSLSSPGVCPTIKLGR-----RLRERGVRCLVY 708
+ F +P + SP + L R L G L Y
Sbjct: 107 SQPLFAFEWEGQQYTFTRLPQGFKN------SPTLFHEA-LARDLAPFPLEHEGTILLQY 159
Query: 709 LDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIPSHRVDYLGISW 760
+DD LLA+ L L LG++V+ KK+Q I V +LG+ W
Sbjct: 160 VDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQ-ICRAEVKFLGVVW 210
Score = 39.3 bits (92), Expect = 0.005
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 15/118 (12%)
Query: 326 NSYVTTKKFKLIN------HQKIP-------LFLQKNDYLATIDLSQAYCHIPIARRHRR 372
N Y + +L+N H +P L K+ + +DL+ A+ +P+A +
Sbjct: 50 NDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPKHQWYTVLDLANAFFSLPLAPDSQP 109
Query: 373 FLCFLYKGTVYQRTCLSFGLASAPQAF--AQLSNWVAVLLRERGVRCLVYLDDFLLAS 428
F ++G Y T L G ++P F A + L G L Y+DD LLA+
Sbjct: 110 LFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAA 167
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy 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. Ty3/Gypsy family widely distributed among
the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 121
Score = 45.5 bits (109), Expect = 9e-06
Identities = 33/127 (25%), Positives = 57/127 (44%), Gaps = 19/127 (14%)
Query: 64 FMSTDASDVGWGAMVGNVSVQGVW----------TQAQRSWHINLKELFTVRAAISSNPS 113
+ TDASD G GA++ + G T A+R++ KEL + A+
Sbjct: 1 VLETDASDFGIGAVLSQL-DDGKERPIAFASRKLTPAERNYSTYEKELLAIVFALKKFRH 59
Query: 114 LVANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNS 173
+ + +D+K++ Y+ + L + LL++ + + I + PGK N
Sbjct: 60 YLLGRKFTVYTDHKSLK-YLLTKKDLN-----PRLARWLLLLQEFDFEIE--YRPGKENV 111
Query: 174 LADALSR 180
+ADALSR
Sbjct: 112 VADALSR 118
Score = 45.5 bits (109), Expect = 9e-06
Identities = 33/127 (25%), Positives = 57/127 (44%), Gaps = 19/127 (14%)
Query: 810 FMSTDASDVGWGAMVGNVSVQGVW----------TQAQRSWHINLKELFTVRAAISSNPS 859
+ TDASD G GA++ + G T A+R++ KEL + A+
Sbjct: 1 VLETDASDFGIGAVLSQL-DDGKERPIAFASRKLTPAERNYSTYEKELLAIVFALKKFRH 59
Query: 860 LVANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNS 919
+ + +D+K++ Y+ + L + LL++ + + I + PGK N
Sbjct: 60 YLLGRKFTVYTDHKSLK-YLLTKKDLN-----PRLARWLLLLQEFDFEIE--YRPGKENV 111
Query: 920 LADALSR 926
+ADALSR
Sbjct: 112 VADALSR 118
Score = 36.7 bits (86), Expect = 0.012
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 467 HTVVLQSDNKTVITYIRKQVGLRSNALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADA 526
+ +D+K+ + Y+ + L N LA + LL++ + + I + PGK N +ADA
Sbjct: 64 RKFTVYTDHKS-LKYLLTKKDL--NPRLA---RWLLLLQEFDFEIE--YRPGKENVVADA 115
Query: 527 LSR 529
LSR
Sbjct: 116 LSR 118
>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 = 38.3 bits (90), Expect = 0.002
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 118 HTVVLQSDNKTVIAYIRKQGGLRSH--ALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLA 175
++++SD++ V+ I+ + RS ALL E +KLL +++ +P +CN +A
Sbjct: 23 RRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDSVSVS----HVPRECNRVA 78
Query: 176 DALSRQAL 183
DAL++ A
Sbjct: 79 DALAKLAS 86
Score = 38.3 bits (90), Expect = 0.002
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 864 HTVVLQSDNKTVIAYIRKQGGLRSH--ALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLA 921
++++SD++ V+ I+ + RS ALL E +KLL +++ +P +CN +A
Sbjct: 23 RRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDSVSVS----HVPRECNRVA 78
Query: 922 DALSRQAL 929
DAL++ A
Sbjct: 79 DALAKLAS 86
Score = 37.9 bits (89), Expect = 0.002
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 467 HTVVLQSDNKTVITYIRKQVGLRSN--ALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLA 524
++++SD++ V+ I+ + RS ALL E +KLL +++ +P +CN +A
Sbjct: 23 RRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKFDSVSVS----HVPRECNRVA 78
Query: 525 DALSRQAL 532
DAL++ A
Sbjct: 79 DALAKLAS 86
>gnl|CDD|238823 cd01645, RT_Rtv, RT_Rtv: Reverse transcriptases (RTs) from
retroviruses (Rtvs). RTs catalyze the conversion of
single-stranded RNA into double-stranded viral DNA for
integration into host chromosomes. Proteins in this
subfamily contain long terminal repeats (LTRs) and are
multifunctional enzymes with RNA-directed DNA
polymerase, DNA directed DNA polymerase, and
ribonuclease hybrid (RNase H) activities. The viral RNA
genome enters the cytoplasm as part of a nucleoprotein
complex, and the process of reverse transcription
generates in the cytoplasm forming a linear DNA duplex
via an intricate series of steps. This duplex DNA is
colinear with its RNA template, but contains terminal
duplications known as LTRs that are not present in viral
RNA. It has been proposed that two specialized template
switches, known as strand-transfer reactions or "jumps",
are required to generate the LTRs.
Length = 213
Score = 40.3 bits (95), Expect = 0.002
Identities = 31/137 (22%), Positives = 53/137 (38%), Gaps = 19/137 (13%)
Query: 637 PLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFLIPMDMSSFRPS------------LS 684
P L K L +DL + IP+ R F +P +++ P+ +
Sbjct: 77 PAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVP-SINNKGPAKRYQWKVLPQGMKN 135
Query: 685 SPGVCPTI--KLGRRLRERGVRCLV--YLDDFLLASQDPIVLKNQILQTLQLLTYLGWQV 740
SP +C + + R++ ++ Y+DD L+AS L+ + Q L G +
Sbjct: 136 SPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTI 195
Query: 741 NLKKSQIIPSHRVDYLG 757
+K Q YLG
Sbjct: 196 PPEKVQK--EPPFQYLG 210
Score = 29.6 bits (67), Expect = 5.8
Identities = 24/102 (23%), Positives = 36/102 (35%), Gaps = 17/102 (16%)
Query: 343 PLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFLYKGTV-----------YQRTCLSFG 391
P L K L +DL + IP+ R F TV YQ L G
Sbjct: 77 PAALPKGWPLIVLDLKDCFFSIPLHPDDRERFAF----TVPSINNKGPAKRYQWKVLPQG 132
Query: 392 LASAPQAFAQLSNWVAVLLRERGVRCLV--YLDDFLLASQDS 431
+ ++P R++ ++ Y+DD L+AS
Sbjct: 133 MKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE 174
>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 = 33.6 bits (78), Expect = 0.14
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 119 TVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADAL 178
+ + D++ V+ I+ + +++ L ++ ++ K + + IP + N ADAL
Sbjct: 64 KLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKW-IPREENKEADAL 122
Query: 179 SRQAL 183
+ QAL
Sbjct: 123 ANQAL 127
Score = 33.6 bits (78), Expect = 0.14
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 865 TVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADAL 924
+ + D++ V+ I+ + +++ L ++ ++ K + + IP + N ADAL
Sbjct: 64 KLEIYGDSQLVVNQIQGEYEVKNERLAPYLEEARELLKKFEEVEIKW-IPREENKEADAL 122
Query: 925 SRQAL 929
+ QAL
Sbjct: 123 ANQAL 127
Score = 32.5 bits (75), Expect = 0.32
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 11/70 (15%)
Query: 468 TVVLQSDNKTVI-----TYIRKQVGLRSNALLAETKKLLLIMSKLNIHIVPYFIPGKCNS 522
+ + D++ V+ Y K L L E ++LL ++ I +IP + N
Sbjct: 64 KLEIYGDSQLVVNQIQGEYEVKNERLAP--YLEEARELLKKFEEVEIK----WIPREENK 117
Query: 523 LADALSRQAL 532
ADAL+ QAL
Sbjct: 118 EADALANQAL 127
>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 = 33.8 bits (78), Expect = 0.31
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 695 GRRLRERGVRCLVYLDDFLLASQDPIVLKNQILQTLQ-LLTYLGWQVNLKKSQIIPSHRV 753
+L G+ L Y DD +L S+ ++LQ LQ G ++N KS+++
Sbjct: 134 EIKLGGPGITHLAYADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVMLIGNK 193
Query: 754 D 754
Sbjct: 194 K 194
>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 = 30.4 bits (69), Expect = 2.2
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 701 RGVRCLVYLDDFLLASQDPIVLKNQILQTLQ-LLTYLGWQVNLKKSQIIPS----HRVDY 755
+GV + Y+DD + + + +IL+ L+ L LG +NL K++I+P D+
Sbjct: 81 KGVDYVRYVDDIRIFADSKEEAE-EILEELKEFLAELGLSLNLSKTEILPLPEGTASKDF 139
Query: 756 LG 757
LG
Sbjct: 140 LG 141
>gnl|CDD|197211 cd09112, PLDc_CLS_2, catalytic domain repeat 2 of bacterial
cardiolipin synthase and similar proteins. This CD
corresponds to the catalytic domain repeat 2 of
bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-)
and a few homologs found in eukaryotes and archea.
Bacterial CL synthases catalyze reversible phosphatidyl
group transfer between two phosphatidylglycerol
molecules to form cardiolipin (CL) and glycerol. The
monomer of bacterial CL synthase consists of two
catalytic domains. Each catalytic domain contains one
copy of conserved HKD motifs (H-X-K-X(4)-D, X represents
any amino acid residue) that are the characteristic of
the phospholipase D (PLD) superfamily. Two HKD motifs
from two domains together form a single active site
involving in phosphatidyl group transfer. Bacterial CL
synthases can be stimulated by phosphate and inhibited
by CL, the product of the reaction, and by
phosphatidate. Phosphate stimulation may be unique to
enzymes with CL synthase activity in PLD superfamily.
Like other PLD enzymes, bacterial CL synthase utilize a
common two-step ping-pong catalytic mechanism involving
an enzyme-substrate intermediate to cleave
phosphodiester bonds. The two histidine residues from
the two HKD motifs play key roles in the catalysis. Upon
substrate binding, a histidine residue from one HKD
motif could function as the nucleophile attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid stabilizing the leaving group.
Length = 174
Score = 30.1 bits (69), Expect = 3.3
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 14/60 (23%)
Query: 502 LIMS-KLNIHIV-PYFIPGKCNSLADALSRQAL------IPDWHLLPSLTESVFPRWGSR 553
I S K +I+I PYFIP SL +AL AL I ++P + W SR
Sbjct: 19 AINSAKKSIYIQTPYFIPD--ESLLEALKTAALSGVDVRI----MIPGKPDHKLVYWASR 72
>gnl|CDD|236085 PRK07740, PRK07740, hypothetical protein; Provisional.
Length = 244
Score = 30.0 bits (68), Expect = 5.4
Identities = 25/96 (26%), Positives = 34/96 (35%), Gaps = 35/96 (36%)
Query: 589 PPLLQVLHHLNDAQGLYGDG--------------------TMRPVFNLKSLNSYVTTKKF 628
PPL +VLH G G T R F + ++ T
Sbjct: 126 PPLAEVLHRFYA---FIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLID---TMFLT 179
Query: 629 KLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRH 664
KL+ H++ T+D + AY IPI RRH
Sbjct: 180 KLLAHER---------DFPTLDDALAYYGIPIPRRH 206
>gnl|CDD|216958 pfam02278, Lyase_8, Polysaccharide lyase family 8, super-sandwich
domain. This family consists of a group of secreted
bacterial lyase enzymes EC:4.2.2.1 capable of acting on
hyaluronan and chondroitin in the extracellular matrix
of host tissues, contributing to the invasive capacity
of the pathogen.
Length = 269
Score = 29.5 bits (66), Expect = 8.4
Identities = 16/112 (14%), Positives = 32/112 (28%)
Query: 61 PRTFMSTDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTV 120
D + A + + A++SW ++ + A I S T
Sbjct: 102 KSNDFVGGKLDDVYAAAGMDFTNWDDTLTAKKSWFFLDDKIVFLGAGIKSTDPENNVTTT 161
Query: 121 VLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCN 172
+ N +V Y + A+ + + S + Y+ N
Sbjct: 162 IDNRKNGSVNGYTGYTNDKKITLFKAQETNSVFLESWDLKKNIGYYFFKGSN 213
Score = 29.5 bits (66), Expect = 8.4
Identities = 16/112 (14%), Positives = 32/112 (28%)
Query: 807 PRTFMSTDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTV 866
D + A + + A++SW ++ + A I S T
Sbjct: 102 KSNDFVGGKLDDVYAAAGMDFTNWDDTLTAKKSWFFLDDKIVFLGAGIKSTDPENNVTTT 161
Query: 867 VLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCN 918
+ N +V Y + A+ + + S + Y+ N
Sbjct: 162 IDNRKNGSVNGYTGYTNDKKITLFKAQETNSVFLESWDLKKNIGYYFFKGSN 213
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.419
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 48,597,945
Number of extensions: 4802679
Number of successful extensions: 3645
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3623
Number of HSP's successfully gapped: 33
Length of query: 960
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 854
Effective length of database: 6,236,078
Effective search space: 5325610612
Effective search space used: 5325610612
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: 64 (28.3 bits)