Query psy14859
Match_columns 1097
No_of_seqs 441 out of 2402
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 22:34:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14859hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd03715 RT_ZFREV_like RT_ZFREV 100.0 1.4E-41 3E-46 364.4 15.0 206 452-668 1-210 (210)
2 cd01645 RT_Rtv RT_Rtv: Reverse 100.0 2.6E-38 5.6E-43 339.8 15.2 201 452-668 1-213 (213)
3 cd01647 RT_LTR RT_LTR: Reverse 100.0 1.4E-30 3E-35 267.3 10.1 177 487-668 1-177 (177)
4 cd01644 RT_pepA17 RT_pepA17: R 99.9 5.4E-28 1.2E-32 259.1 6.3 168 498-670 2-189 (213)
5 cd03714 RT_DIRS1 RT_DIRS1: Rev 99.9 2.2E-25 4.9E-30 217.8 9.3 118 551-668 1-119 (119)
6 PF00078 RVT_1: Reverse transc 99.6 8.3E-16 1.8E-20 163.4 9.0 164 505-668 1-214 (214)
7 cd00304 RT_like RT_like: Rever 99.3 1.6E-12 3.4E-17 122.1 7.6 94 551-668 1-98 (98)
8 PF09337 zf-H2C2: His(2)-Cys(2 99.1 8.8E-11 1.9E-15 91.3 3.1 37 955-991 3-39 (39)
9 cd03487 RT_Bac_retron_II RT_Ba 98.9 6.4E-09 1.4E-13 112.3 9.1 141 543-685 54-210 (214)
10 cd01648 TERT TERT: Telomerase 98.8 7.1E-09 1.5E-13 101.7 6.6 104 551-669 1-119 (119)
11 PF00336 DNA_pol_viral_C: DNA 98.8 1.4E-08 3.1E-13 104.2 8.6 186 678-891 8-194 (245)
12 cd01650 RT_nLTR_like RT_nLTR: 98.8 7.4E-09 1.6E-13 111.4 5.6 100 544-656 80-188 (220)
13 cd06222 RnaseH RNase H (RNase 98.7 2E-08 4.4E-13 96.4 7.1 116 773-890 1-128 (130)
14 cd01651 RT_G2_intron RT_G2_int 98.6 6.9E-08 1.5E-12 104.1 7.3 127 542-668 66-226 (226)
15 PRK13907 rnhA ribonuclease H; 98.4 3.4E-07 7.3E-12 90.8 7.0 116 772-890 2-123 (128)
16 cd01646 RT_Bac_retron_I RT_Bac 98.4 2.4E-07 5.2E-12 95.3 4.7 93 579-671 49-147 (158)
17 PF00075 RNase_H: RNase H; In 98.3 3.8E-07 8.3E-12 90.2 3.8 112 770-889 2-128 (132)
18 COG0328 RnhA Ribonuclease HI [ 98.2 3.1E-06 6.8E-11 85.9 7.4 119 770-890 2-141 (154)
19 PRK07708 hypothetical protein; 98.2 2.2E-06 4.7E-11 92.7 6.5 121 770-890 72-204 (219)
20 PRK07238 bifunctional RNase H/ 98.0 9E-06 1.9E-10 95.3 7.4 118 771-890 2-128 (372)
21 PF13456 RVT_3: Reverse transc 98.0 9.6E-06 2.1E-10 73.9 5.3 82 806-890 2-83 (87)
22 PRK00203 rnhA ribonuclease H; 98.0 1.1E-05 2.3E-10 82.5 6.1 115 771-890 3-138 (150)
23 PRK06548 ribonuclease H; Provi 97.9 3E-05 6.5E-10 79.9 7.8 114 770-890 4-138 (161)
24 PRK08719 ribonuclease H; Revie 97.5 0.00014 2.9E-09 74.2 6.0 113 770-890 3-143 (147)
25 PF05380 Peptidase_A17: Pao re 97.3 0.0002 4.4E-09 73.9 4.3 115 702-823 9-144 (159)
26 KOG3752|consensus 96.5 0.0066 1.4E-07 69.3 8.1 118 771-891 212-362 (371)
27 cd01709 RT_like_1 RT_like_1: A 95.7 0.046 1E-06 62.6 9.6 125 581-711 81-225 (346)
28 PF07727 RVT_2: Reverse transc 94.3 0.022 4.7E-07 63.2 1.9 126 545-681 76-222 (246)
29 KOG4768|consensus 91.6 0.24 5.3E-06 59.6 5.3 137 535-671 349-563 (796)
30 cd06094 RP_Saci_like RP_Saci_l 88.4 0.42 9.1E-06 44.5 3.1 73 303-378 3-89 (89)
31 PF02160 Peptidase_A3: Caulifl 85.4 0.28 6.1E-06 52.3 0.3 55 316-370 87-143 (201)
32 cd01699 RNA_dep_RNAP RNA_dep_R 70.2 8.6 0.00019 42.9 6.3 59 610-669 194-255 (278)
33 PF06817 RVT_thumb: Reverse tr 63.3 1.3 2.7E-05 39.6 -1.7 34 696-731 13-46 (70)
34 KOG1005|consensus 59.4 18 0.00038 46.2 6.4 77 580-656 631-713 (888)
35 KOG0307|consensus 43.1 1.3E+02 0.0029 39.7 10.5 119 90-238 837-955 (1049)
36 COG0313 Predicted methyltransf 42.1 14 0.00031 41.4 1.8 66 31-118 65-133 (275)
37 PF05919 Mitovir_RNA_pol: Mito 41.6 54 0.0012 39.8 6.4 152 499-656 85-278 (498)
38 KOG1985|consensus 33.5 1.4E+02 0.0029 38.5 8.3 30 1018-1047 762-791 (887)
39 PF00680 RdRP_1: RNA dependent 32.3 52 0.0011 40.3 4.7 58 611-669 344-406 (491)
40 KOG0162|consensus 30.4 1.1E+02 0.0025 38.6 6.8 13 120-132 990-1002(1106)
41 PHA00028 rep RNA replicase, be 29.0 78 0.0017 38.5 5.0 39 611-656 334-372 (561)
42 KOG4525|consensus 21.1 71 0.0015 37.9 2.7 33 11-44 112-144 (614)
No 1
>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.
Probab=100.00 E-value=1.4e-41 Score=364.36 Aligned_cols=206 Identities=26% Similarity=0.456 Sum_probs=194.9
Q ss_pred CccCCCCCCCccccccCCcccHHHHHHHHHHHHHcCCccccCCCCCcceeEEEEecCCC-CcccccccCCcccccCCccc
Q psy14859 452 PFSAKPPLVPLCSLQHLATPVSSAMSLHIQEMLETGVLKRLDSTTGFLSRLFLVPKGNG-GTRPVLNLKGLNQFLSPKKF 530 (1097)
Q Consensus 452 pv~~~p~r~p~~~lr~~s~~~~~~i~~eI~~ll~~GiI~~~~s~S~~~SPv~~V~Kkdg-k~R~vvD~R~LN~~t~~~~~ 530 (1097)
|+.+++|++++ +++++++++|++|+++|+|+++ .|+|.+|+++|+||+| ++|+|+|||.||+.+..+.+
T Consensus 1 ~~~~~~~~~~~--------~~~~~~~~~v~~ll~~G~I~~~--~s~~~sp~~~V~Kk~g~~~R~~vD~r~lN~~~~~~~~ 70 (210)
T cd03715 1 PVNQKQYPLPR--------EAREGITPHIQELLEAGILVPC--QSPWNTPILPVKKPGGNDYRMVQDLRLVNQAVLPIHP 70 (210)
T ss_pred CCCcCCCCCCH--------HHHHHHHHHHHHHHHCCCeECC--CCCCCCceEEEEeCCCCcceEEEEhhhhhhcccccCc
Confidence 67788888877 4568999999999999999995 8999999999999999 99999999999999999999
Q ss_pred ccccccccccccc-CCceeEEecccccccccccccccccccccccccceEEeeccCccCCCChHHHHHhhHHHHhhhhc-
Q psy14859 531 SLINHFRIPSFLQ-KGDYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAMTCLPFGLATAPQAFASLSNWVASLLRS- 608 (1097)
Q Consensus 531 plP~i~~ll~~L~-~~~~fs~lDLksAY~qI~L~~edr~~taF~t~~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~- 608 (1097)
++|++++++..+. ++++|+++|+++|||||+|+++++++|+|++++|+|+|++||||+++||++||++|+.++..+..
T Consensus 71 ~~p~~~~~l~~l~~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~y~~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~ 150 (210)
T cd03715 71 AVPNPYTLLSLLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLE 150 (210)
T ss_pred CCCcHHHHHHHhccCCeEEEEeeccCeEEEEEcccccEEeEEEEECCeeEEEEEEeccccCcHHHHHHHHHHHHHHHHhh
Confidence 9999999999996 79999999999999999999999999999999999999999999999999999999999997743
Q ss_pred -cCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCCCCCeEEEeeEEe
Q psy14859 609 -RGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLSPAPVLQFLGIMW 668 (1097)
Q Consensus 609 -~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~p~~~v~fLG~iI 668 (1097)
.+..+.+|+|||+|++++.++|.++++.|+.+|+++|+.+|++||+++ .++++||||+|
T Consensus 151 ~~~~~~~~Y~DDili~s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~-~~~v~fLG~~~ 210 (210)
T cd03715 151 HEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQIC-RAEVKFLGVVW 210 (210)
T ss_pred CCCeEEEEECCcEEEecCCHHHHHHHHHHHHHHHHHCCCCcCHHHeeCC-CCceEEeeEEC
Confidence 356789999999999999999999999999999999999999999998 99999999986
No 2
>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.
Probab=100.00 E-value=2.6e-38 Score=339.78 Aligned_cols=201 Identities=20% Similarity=0.282 Sum_probs=180.5
Q ss_pred CccCCCCCCCccccccCCcccHHHHHHHHHHHHHcCCccccCCCCCcceeEEEEecCCCCcccccccCCcccccCCccc-
Q psy14859 452 PFSAKPPLVPLCSLQHLATPVSSAMSLHIQEMLETGVLKRLDSTTGFLSRLFLVPKGNGGTRPVLNLKGLNQFLSPKKF- 530 (1097)
Q Consensus 452 pv~~~p~r~p~~~lr~~s~~~~~~i~~eI~~ll~~GiI~~~~s~S~~~SPv~~V~Kkdgk~R~vvD~R~LN~~t~~~~~- 530 (1097)
||..+.|++++ +++++++++|++|+++|+|+++ .|+|.+|+++|+|++|++|+|+|||.||+.+.++.+
T Consensus 1 ~~~~~~~p~~~--------~~~~~~~~~i~~ll~~g~I~~~--~s~~~sp~~~v~K~~g~~R~~~D~r~lN~~~~~~~~~ 70 (213)
T cd01645 1 PVWIKQWPLTE--------EKLEALTELVTEQLKEGHIEPS--TSPWNTPVFVIKKKSGKWRLLHDLRAVNAQTQDMGAL 70 (213)
T ss_pred CCCCCccCCCH--------HHHHHHHHHHHHHHHCCceecC--CCCCcCcEEEEEcCCCCeEEEechHHHhhhccccccc
Confidence 56666676666 5668999999999999999995 699999999999999999999999999999987654
Q ss_pred --cccccccccccccCCceeEEecccccccccccccccccccccccc-------cceEEeeccCccCCCChHHHHHhhHH
Q psy14859 531 --SLINHFRIPSFLQKGDYMISIDLSQAYFHVPIKTTHQRFLALSYN-------GDVLAMTCLPFGLATAPQAFASLSNW 601 (1097)
Q Consensus 531 --plP~i~~ll~~L~~~~~fs~lDLksAY~qI~L~~edr~~taF~t~-------~g~y~~~rLPFGL~nSP~~Fqr~m~~ 601 (1097)
++|.. ..+.++.+|+++|+++|||||+|+++++++|+|.++ +|.|+|++||||+++||++||++|+.
T Consensus 71 ~~~~p~~----~~l~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~~~~~~~~~~~~~lP~Gl~~SP~~f~~~m~~ 146 (213)
T cd01645 71 QPGLPHP----AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQ 146 (213)
T ss_pred CCCCCCh----HHcCCCceEEEEEccCcEEEeeeccCCcceeEEEeccccCCCCCceEEEEEeCCCCcChHHHHHHHHHH
Confidence 23332 457888999999999999999999999999999985 79999999999999999999999999
Q ss_pred HHhhhhcc--CceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCCCCCeEEEeeEEe
Q psy14859 602 VASLLRSR--GMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLSPAPVLQFLGIMW 668 (1097)
Q Consensus 602 il~~lr~~--g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~p~~~v~fLG~iI 668 (1097)
++..++.. +..+..|+|||+|++++.++|.++++.|+++|+++|+.+|++||++. .+++||||.|
T Consensus 147 ~l~~~~~~~~~~~~~~Y~DDili~s~~~~~~~~~l~~v~~~l~~~gl~ln~~K~~~~--~~v~fLG~~i 213 (213)
T cd01645 147 ALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPEKVQKE--PPFQYLGYEL 213 (213)
T ss_pred HHHHHHHHCCCeEEEEEcCCEEEEcCCHHHHHHHHHHHHHHHHHCCCEeCHHHEeCC--CCeEeccEeC
Confidence 99987643 34688999999999999999999999999999999999999999984 6899999986
No 3
>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.
Probab=99.96 E-value=1.4e-30 Score=267.25 Aligned_cols=177 Identities=24% Similarity=0.355 Sum_probs=169.4
Q ss_pred CCccccCCCCCcceeEEEEecCCCCcccccccCCcccccCCccccccccccccccccCCceeEEeccccccccccccccc
Q psy14859 487 GVLKRLDSTTGFLSRLFLVPKGNGGTRPVLNLKGLNQFLSPKKFSLINHFRIPSFLQKGDYMISIDLSQAYFHVPIKTTH 566 (1097)
Q Consensus 487 GiI~~~~s~S~~~SPv~~V~Kkdgk~R~vvD~R~LN~~t~~~~~plP~i~~ll~~L~~~~~fs~lDLksAY~qI~L~~ed 566 (1097)
|+|+++ .++|.+|+++|+|+++++|+|+|+|.+|+.+.++.+++|.+++++..+++..+++++|+.+||+||++++++
T Consensus 1 g~i~~~--~~~~~~p~~~v~k~~~k~R~~~D~r~ln~~~~~~~~~~p~i~~~~~~~~~~~~~~~~D~~~~~~~i~l~~~~ 78 (177)
T cd01647 1 GIIEPS--SSPYASPVVVVKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEES 78 (177)
T ss_pred CeeEcc--CCCCCCceEEEECCCCCEEEEEcCHHHhcccCCCCCCCCCHHHHHHHhhcCcEEEecccccCcceeeeccCC
Confidence 788885 677889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccccceEEeeccCccCCCChHHHHHhhHHHHhhhhccCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccc
Q psy14859 567 QRFLALSYNGDVLAMTCLPFGLATAPQAFASLSNWVASLLRSRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGW 646 (1097)
Q Consensus 567 r~~taF~t~~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl 646 (1097)
+++++|.++++.|.|++||||+++||..|++.|+.++..+. +..+..|+||++|.+.+.++|..+++.++.+|+++|+
T Consensus 79 ~~~~~~~~~~~~~~~~~~p~G~~~s~~~~~~~~~~~l~~~~--~~~~~~y~DDi~i~~~~~~~~~~~~~~~~~~l~~~~~ 156 (177)
T cd01647 79 RPKTAFRTPFGLYEYTRMPFGLKNAPATFQRLMNKILGDLL--GDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGL 156 (177)
T ss_pred hhhceeecCCCccEEEEecCCCccHHHHHHHHHHhhhcccc--ccccEEEecCccccCCCHHHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999998763 3578999999999999999999999999999999999
Q ss_pred eeccccCCCCCCCeEEEeeEEe
Q psy14859 647 IVNLQKSSLSPAPVLQFLGIMW 668 (1097)
Q Consensus 647 ~ln~~Kc~f~p~~~v~fLG~iI 668 (1097)
.+|++||++. .++++||||++
T Consensus 157 ~~~~~K~~~~-~~~~~~lG~~i 177 (177)
T cd01647 157 KLNPEKCEFG-VPEVEFLGHIV 177 (177)
T ss_pred EeCHHHceec-cCceEeeeEEC
Confidence 9999999998 89999999985
No 4
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=99.94 E-value=5.4e-28 Score=259.07 Aligned_cols=168 Identities=18% Similarity=0.205 Sum_probs=154.8
Q ss_pred cceeEEEEecC---CCCcccccccC------CcccccCCccccccccccccccccCCceeEEeccccccccccccccccc
Q psy14859 498 FLSRLFLVPKG---NGGTRPVLNLK------GLNQFLSPKKFSLINHFRIPSFLQKGDYMISIDLSQAYFHVPIKTTHQR 568 (1097)
Q Consensus 498 ~~SPv~~V~Kk---dgk~R~vvD~R------~LN~~t~~~~~plP~i~~ll~~L~~~~~fs~lDLksAY~qI~L~~edr~ 568 (1097)
|..|++.|.|+ .||+|+|+|+| +||+.+.++++++|++.+++.+++++++++++|+++|||||+|+++|+.
T Consensus 2 ~y~ph~~V~~~~~~~~k~R~V~D~s~~~~g~sLN~~l~~gp~~~~~l~~iL~~~R~~~~~~~~Di~~af~qI~i~~~d~~ 81 (213)
T cd01644 2 WYLPHHAVIKPSKTTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRD 81 (213)
T ss_pred cccCCceecCCCCCCCccEEEEecccccCCchhhHHhccCCccccchhhhheeeecCceeEehhHHHhhhheecCcccCc
Confidence 78899999887 58999999999 6999999999999999999999999999999999999999999999999
Q ss_pred cccccccc-------ceEEeeccCccCCCChHHHHHhhHHHHhhhhcc----CceEEEEecCceeeecCchhHHHhhhHH
Q psy14859 569 FLALSYNG-------DVLAMTCLPFGLATAPQAFASLSNWVASLLRSR----GMRVVVYLDDFLLVNQDPRILEIQGKLA 637 (1097)
Q Consensus 569 ~taF~t~~-------g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~~----g~~v~vYvDDILI~s~s~eeh~~~l~~V 637 (1097)
+++|.|.+ +.|+|++||||+++||++||++|+.+++.++.. ...+..|||||++.+++.+||...+++|
T Consensus 82 ~~~F~w~~~~~~~~~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e~~~~~~~v 161 (213)
T cd01644 82 VLRFLWRKDGDEPKPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRL 161 (213)
T ss_pred eEEEEEeCCCCCCcceEEEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCCHHHHHHHHHHH
Confidence 99999865 899999999999999999999999999988642 2246799999999999999999999999
Q ss_pred HHHHhhccceeccccCCCCCCCeEEEeeEEeCC
Q psy14859 638 VSILGSLGWIVNLQKSSLSPAPVLQFLGIMWDP 670 (1097)
Q Consensus 638 l~~L~~~Gl~ln~~Kc~f~p~~~v~fLG~iIs~ 670 (1097)
+++|++.||.+ |.|. ..+.++||.+...
T Consensus 162 ~~~L~~~Gf~l----~kw~-sn~~~~l~~~~~~ 189 (213)
T cd01644 162 IALLKKGGFNL----RKWA-SNSQEVLDDLPEE 189 (213)
T ss_pred HHHHHhCCccc----hhcc-cCchhhhhccccc
Confidence 99999999977 6676 8888999988754
No 5
>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.
Probab=99.92 E-value=2.2e-25 Score=217.81 Aligned_cols=118 Identities=34% Similarity=0.668 Sum_probs=106.1
Q ss_pred ecccccccccccccccccccccccccceEEeeccCccCCCChHHHHHhhHHHHhhhhccCceEEEEecCceeeecCchhH
Q psy14859 551 IDLSQAYFHVPIKTTHQRFLALSYNGDVLAMTCLPFGLATAPQAFASLSNWVASLLRSRGMRVVVYLDDFLLVNQDPRIL 630 (1097)
Q Consensus 551 lDLksAY~qI~L~~edr~~taF~t~~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~~g~~v~vYvDDILI~s~s~eeh 630 (1097)
+|+++|||||+|+++++++|||++++|.|+|+|||||+++||++||++|+.++..++..+..+..|+|||+|++++.+++
T Consensus 1 lD~~~ay~~i~l~~~~~~~~af~~~~~~~~~~~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~~~ 80 (119)
T cd03714 1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSIKTS 80 (119)
T ss_pred CchhhceEEEecCCCCcceeeEEECCCcEEEEecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcHHHH
Confidence 69999999999999999999999999999999999999999999999999999988877788999999999999985555
Q ss_pred HHhhhHHHH-HHhhccceeccccCCCCCCCeEEEeeEEe
Q psy14859 631 EIQGKLAVS-ILGSLGWIVNLQKSSLSPAPVLQFLGIMW 668 (1097)
Q Consensus 631 ~~~l~~Vl~-~L~~~Gl~ln~~Kc~f~p~~~v~fLG~iI 668 (1097)
...++.+.. +++++|+++|++||+++++++++||||+|
T Consensus 81 ~~~~~~l~~~~l~~~gl~ln~~K~~~~~~~~v~fLG~~~ 119 (119)
T cd03714 81 EAVLRHLRATLLANLGFTLNLEKSKLGPTQRITFLGLEL 119 (119)
T ss_pred HHHHHHHHHHHHHHcCCccChhhcEecCCCcEEECcEeC
Confidence 444444444 69999999999999965599999999985
No 6
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=99.62 E-value=8.3e-16 Score=163.41 Aligned_cols=164 Identities=20% Similarity=0.328 Sum_probs=136.5
Q ss_pred EecCC-CCcccc----cccCCcccccCC------------ccccccccccc-----cccccCCceeEEeccccccccccc
Q psy14859 505 VPKGN-GGTRPV----LNLKGLNQFLSP------------KKFSLINHFRI-----PSFLQKGDYMISIDLSQAYFHVPI 562 (1097)
Q Consensus 505 V~Kkd-gk~R~v----vD~R~LN~~t~~------------~~~plP~i~~l-----l~~L~~~~~fs~lDLksAY~qI~L 562 (1097)
|||++ |++|++ +++|.+|+.+.. ..+........ +....+..++.++|+++||++|+.
T Consensus 1 ipK~~~~~~RpI~~~~~~~r~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Di~~~f~sI~~ 80 (214)
T PF00078_consen 1 IPKKNVGKYRPISIPSVDDRIVQRVLNKRLQPILEPIFSPSQFGFRPGRSCHDIKKLNRFKGYLYFLKLDISKAFDSIPH 80 (214)
T ss_dssp EESSSSSSEEEE----EBTHHHHHHBHH---------HHHTTSSCSHGCCCHHHHHHHC-CGSSEEEEEECCCCGGGSBB
T ss_pred CCCcCCCCeeEcCCCCcHHHHHHHHHHhhccccccccCCCCCCCCcccccccccccccccccccccceecccccccccee
Confidence 68999 999998 788866655533 22222222222 446778899999999999999999
Q ss_pred ccccccccccccc------------------------cceEEeeccCccCCCChHHHHHhhHHHHhhhhc---cCceEEE
Q psy14859 563 KTTHQRFLALSYN------------------------GDVLAMTCLPFGLATAPQAFASLSNWVASLLRS---RGMRVVV 615 (1097)
Q Consensus 563 ~~edr~~taF~t~------------------------~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~---~g~~v~v 615 (1097)
+.-.+....+.++ ...+....+|||...||.+|+..|..+.+.+.. .+..+..
T Consensus 81 ~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~r 160 (214)
T PF00078_consen 81 HRLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDLSPYFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLR 160 (214)
T ss_dssp HTTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSSSEEEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEE
T ss_pred eecccccccccccccccccccccccccccccccccccccccccccccccccccchhhccccccccccccccccccccceE
Confidence 9999988888776 457889999999999999999999999998776 4678999
Q ss_pred EecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC-CCCeEEEeeEEe
Q psy14859 616 YLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS-PAPVLQFLGIMW 668 (1097)
Q Consensus 616 YvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~-p~~~v~fLG~iI 668 (1097)
|+||+++.+++.+++...++.+.+.++++|+.+|++||.+. ...+++|||+.|
T Consensus 161 Y~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~~~~~~~~~~~lG~~i 214 (214)
T PF00078_consen 161 YADDILIISKSKEELQKILEKISQWLEELGLKLNPEKTKILHPSDSVKFLGYVI 214 (214)
T ss_dssp ETTEEEEEESSHHHHHHHHHHHHHHHHHTTSBCSSTTTSCS--ESSEEETTEEE
T ss_pred eccccEEEECCHHHHHHHHHHHHHHHHHCCCEEChHHEEEEeCCCCEEEEeEEC
Confidence 99999999999999999999999999999999999999986 478999999986
No 7
>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.
Probab=99.35 E-value=1.6e-12 Score=122.12 Aligned_cols=94 Identities=18% Similarity=0.367 Sum_probs=86.7
Q ss_pred ecccccccccccccccccccccccccceEEeeccCccCCCChHHHHHhhHHHHhhhhc--cCceEEEEecCceeeecCch
Q psy14859 551 IDLSQAYFHVPIKTTHQRFLALSYNGDVLAMTCLPFGLATAPQAFASLSNWVASLLRS--RGMRVVVYLDDFLLVNQDPR 628 (1097)
Q Consensus 551 lDLksAY~qI~L~~edr~~taF~t~~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~--~g~~v~vYvDDILI~s~s~e 628 (1097)
+|++++|+||+ ||||...||.+|+.+|+.+...++. .+..+..|+||+++.+++.
T Consensus 1 ~d~~~~~~~~~----------------------lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~- 57 (98)
T cd00304 1 FDVKSFFTSIP----------------------LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE- 57 (98)
T ss_pred CCHHHcCCCCc----------------------cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-
Confidence 59999999998 9999999999999999999988754 3668999999999999998
Q ss_pred hHHHhhhHHHHHHhhccceeccccCCC--CCCCeEEEeeEEe
Q psy14859 629 ILEIQGKLAVSILGSLGWIVNLQKSSL--SPAPVLQFLGIMW 668 (1097)
Q Consensus 629 eh~~~l~~Vl~~L~~~Gl~ln~~Kc~f--~p~~~v~fLG~iI 668 (1097)
++...+..+.+.++++|+.+|++||++ . .++++|||+++
T Consensus 58 ~~~~~~~~l~~~l~~~gl~ln~~Kt~~~~~-~~~~~flG~~~ 98 (98)
T cd00304 58 QQAVKKRELEEFLARLGLNLSDEKTQFTEK-EKKFKFLGILV 98 (98)
T ss_pred HHHHHHHHHHHHHHHcCcEEChheeEEecC-CCCeeeeceeC
Confidence 899999999999999999999999998 6 89999999975
No 8
>PF09337 zf-H2C2: His(2)-Cys(2) zinc finger; InterPro: IPR015416 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents an H2C2-type zinc finger that binds to histone upstream activating sequence (UAS) elements found in histone gene promoters []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=99.06 E-value=8.8e-11 Score=91.30 Aligned_cols=37 Identities=14% Similarity=0.021 Sum_probs=35.5
Q ss_pred CCCCChHHhHHHhhccccCCCcHHHHHHHhhcchhhh
Q psy14859 955 SLDPDHFQELDDFVVFWPVFGSKTDSSSHLQSGWKIK 991 (1097)
Q Consensus 955 ~GH~G~~kT~~rl~~~f~Wp~M~~dV~~yV~~C~~~~ 991 (1097)
.||+|+.||+.+|+++||||||++||++||++|..|+
T Consensus 3 ~~H~Gi~kT~~~i~~~y~W~gm~~~V~~~ir~C~~Cq 39 (39)
T PF09337_consen 3 QGHPGINKTTAKISQRYHWPGMKKDVRRVIRSCPQCQ 39 (39)
T ss_pred ccCCCHHHHHHHHHHhheecCHHHHHHHHHhcCcccC
Confidence 4699999999999999999999999999999999996
No 9
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: 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.
Probab=98.85 E-value=6.4e-09 Score=112.29 Aligned_cols=141 Identities=18% Similarity=0.279 Sum_probs=103.2
Q ss_pred cCCceeEEecccccccccccccccccccccccc-c-------ceE-EeeccCccCCCChHHHHHhhHHHHhhhh----cc
Q psy14859 543 QKGDYMISIDLSQAYFHVPIKTTHQRFLALSYN-G-------DVL-AMTCLPFGLATAPQAFASLSNWVASLLR----SR 609 (1097)
Q Consensus 543 ~~~~~fs~lDLksAY~qI~L~~edr~~taF~t~-~-------g~y-~~~rLPFGL~nSP~~Fqr~m~~il~~lr----~~ 609 (1097)
.+..++.++|++++|.+|..+.--+........ . ... .-..+|+|...||.++.-+|..+...+. ..
T Consensus 54 ~~~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l~~~~~~~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~ 133 (214)
T cd03487 54 CGAKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVATILAKLCTYNGHLPQGAPTSPALSNLVFRKLDERLSKLAKSN 133 (214)
T ss_pred cCCCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHHHHHHHHHhCCCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHc
Confidence 467899999999999999765421111111110 0 000 0128999999999999999887666543 34
Q ss_pred CceEEEEecCceeeecCch--hHHHhhhHHHHHHhhccceeccccCCCCC-CCeEEEeeEEeCCCCCcccCcchhhhhh
Q psy14859 610 GMRVVVYLDDFLLVNQDPR--ILEIQGKLAVSILGSLGWIVNLQKSSLSP-APVLQFLGIMWDPHLDRMWLPEDKQLTL 685 (1097)
Q Consensus 610 g~~v~vYvDDILI~s~s~e--eh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~p-~~~v~fLG~iIs~~gi~v~l~~~Ki~ai 685 (1097)
|.....|+||++|++++.+ +....+..+-..|++.|+.+|++|+.... .....|||+.++.+.+++ +.++...+
T Consensus 134 ~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~~~~~~~G~~i~~~~~~~--~~~~~~~i 210 (214)
T cd03487 134 GLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKTRISSKGSRQIVTGLVVNNGKPSL--PRKEKRKI 210 (214)
T ss_pred CCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCceEEccCCCCcEEEEEEEeCCcCCC--CHHHHHHH
Confidence 6788999999999999887 67777788888888999999999998762 368999999999886644 55555433
No 10
>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
Probab=98.80 E-value=7.1e-09 Score=101.66 Aligned_cols=104 Identities=15% Similarity=0.205 Sum_probs=86.4
Q ss_pred ecccccccccccccccccccccccccceEEe-eccCccCCCChHHHHHhhHHHHhhhhcc------CceEEEEecCceee
Q psy14859 551 IDLSQAYFHVPIKTTHQRFLALSYNGDVLAM-TCLPFGLATAPQAFASLSNWVASLLRSR------GMRVVVYLDDFLLV 623 (1097)
Q Consensus 551 lDLksAY~qI~L~~edr~~taF~t~~g~y~~-~rLPFGL~nSP~~Fqr~m~~il~~lr~~------g~~v~vYvDDILI~ 623 (1097)
.|++++|=+|+. .|.. +.+|+|...||.+|.-.|+.+.+.+... +...+.|+||++++
T Consensus 1 ~d~~~~~~~~~~---------------~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~ 65 (119)
T cd01648 1 TDIKKCYDSIPQ---------------YYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLI 65 (119)
T ss_pred CChHHhccchhh---------------hhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEE
Confidence 488999999987 3333 3599999999999999988887765432 44678999999999
Q ss_pred ecCchhHHHhhhHHHHHH-hhccceeccccCCCC-------CCCeEEEeeEEeC
Q psy14859 624 NQDPRILEIQGKLAVSIL-GSLGWIVNLQKSSLS-------PAPVLQFLGIMWD 669 (1097)
Q Consensus 624 s~s~eeh~~~l~~Vl~~L-~~~Gl~ln~~Kc~f~-------p~~~v~fLG~iIs 669 (1097)
+.+.++..+.+..+.+.+ ++.|+.+|++|++.. +.+.+.||||.|+
T Consensus 66 ~~~~~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~~~~~~~~~~~~~~flG~~i~ 119 (119)
T cd01648 66 TTSLDKAIKFLNLLLRGFINQYKTFVNFDKTQINFSFAQLDSSDLIPWCGLLIN 119 (119)
T ss_pred eCCHHHHHHHHHHHHHhhHHhhCeEECcccceeeccccccCCCCccCceeEeeC
Confidence 999988888888888887 999999999999863 3677899999885
No 11
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=98.79 E-value=1.4e-08 Score=104.17 Aligned_cols=186 Identities=21% Similarity=0.236 Sum_probs=132.2
Q ss_pred cchhhhhhhHHHHHhhhccccChhhhhhhhhccccccccccCCccchhhhHHHHHHhhcCCCCCCCCCcccchhhHHhhh
Q psy14859 678 PEDKQLTLGNILRTLLASKTWNLDSARSLLGYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLTPINPAVLPKLEWWLN 757 (1097)
Q Consensus 678 ~~~Ki~ai~~~~~il~~~~P~t~keLrsfLGllny~r~fI~~~~~~arpL~~ll~~lkk~~~~W~~~~q~Af~~LK~~l~ 757 (1097)
.++.++.|+...+.+.-..|.+.|-.|++.|++||...|-..+-....|||.... .+..|.+++..+.-.-++-
T Consensus 8 qdh~~~kik~~~rKlpvnrpiDwKvcQRivGlLgF~aPFTqcgy~aL~PlY~~iq--~k~aF~FS~~Yk~~L~kqy---- 81 (245)
T PF00336_consen 8 QDHIVQKIKQCFRKLPVNRPIDWKVCQRIVGLLGFAAPFTQCGYPALMPLYAAIQ--SKQAFTFSPTYKAFLCKQY---- 81 (245)
T ss_pred HHHHHHHHHHHHhcCCCCCCcchHHHHhhhhhhhcccccccCCchhhhhHHHHHh--hhheeecCHHHHHHHHHhh----
Confidence 4455667888888887788999999999999999999999999999999998654 4556665544332222211
Q ss_pred hCCCCCCCC-CCCcceeeeeccCCCCCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcH
Q psy14859 758 ALPLSSPIF-PRQVQHFISTDASDLGWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQ 836 (1097)
Q Consensus 758 ~l~~~~Pil-~~~~p~~L~TDAS~~GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk 836 (1097)
...-|+- .+..--.+++||+.+|||.++....+.++|+.. .+|+-.||+|..+|-. ..|.++ +.|||.
T Consensus 82 --~~l~pvarqr~~lc~VfaDATpTgwgi~i~~~~~~~Tfs~~---l~IhtaELlaaClAr~-----~~~~r~-l~tDnt 150 (245)
T PF00336_consen 82 --MNLYPVARQRPGLCQVFADATPTGWGISITGQRMRGTFSKP---LPIHTAELLAACLARL-----MSGARC-LGTDNT 150 (245)
T ss_pred --ccccccccCCCCCCceeccCCCCcceeeecCceeeeeeccc---ccchHHHHHHHHHHHh-----ccCCcE-EeecCc
Confidence 1112221 222345789999999999998887777887763 5899999999987743 345555 889998
Q ss_pred HHHHHHHhcCCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCccccccccCCC
Q psy14859 837 TVVSYLRRQGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNSVADSLSRSK 891 (1097)
Q Consensus 837 ~lv~~l~~~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~~ADaLSR~~ 891 (1097)
.+++ ++ -............|+.+ + ..+.|||++.| .||.-||..
T Consensus 151 ~Vls---rk----yts~PW~lac~A~wiLr-g--ts~~yVPS~~N-PAD~PsR~~ 194 (245)
T PF00336_consen 151 VVLS---RK----YTSFPWLLACAANWILR-G--TSFYYVPSKYN-PADDPSRGK 194 (245)
T ss_pred EEEe---cc----cccCcHHHHHHHHHhhc-C--ceEEEeccccC-cCCCCCCCc
Confidence 7742 22 22233555555556554 3 34599999999 999999983
No 12
>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.
Probab=98.76 E-value=7.4e-09 Score=111.41 Aligned_cols=100 Identities=19% Similarity=0.195 Sum_probs=84.9
Q ss_pred CCceeEEecccccccccccccccccccccccccceEEeeccCccCCCChHHHHHhhHHHHhhhh--------ccCceEEE
Q psy14859 544 KGDYMISIDLSQAYFHVPIKTTHQRFLALSYNGDVLAMTCLPFGLATAPQAFASLSNWVASLLR--------SRGMRVVV 615 (1097)
Q Consensus 544 ~~~~fs~lDLksAY~qI~L~~edr~~taF~t~~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr--------~~g~~v~v 615 (1097)
+..++.++|+++||..|+.+.-.... .+|+|...||.+|.-+|..+.+.+. ..+..+..
T Consensus 80 ~~~~~l~~Di~~aFdsi~~~~l~~~l-------------GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~ 146 (220)
T cd01650 80 KSLVLVFLDFEKAFDSVDHEFLLKAL-------------GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLA 146 (220)
T ss_pred CceEEEEEEHHhhcCcCCHHHHHHHh-------------CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEE
Confidence 45789999999999998754322222 8999999999999999999988775 34567899
Q ss_pred EecCceeeecCch-hHHHhhhHHHHHHhhccceeccccCCCC
Q psy14859 616 YLDDFLLVNQDPR-ILEIQGKLAVSILGSLGWIVNLQKSSLS 656 (1097)
Q Consensus 616 YvDDILI~s~s~e-eh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~ 656 (1097)
|+||+++++.+.+ .....+..+...+.+.|+.+|++||.+.
T Consensus 147 yaDD~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in~~Kt~~~ 188 (220)
T cd01650 147 YADDIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVM 188 (220)
T ss_pred eccceeeeccCCHHHHHHHHHHHHHHHHHcCCEEChhheEEE
Confidence 9999999999998 7888888888999999999999999865
No 13
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.73 E-value=2e-08 Score=96.43 Aligned_cols=116 Identities=26% Similarity=0.244 Sum_probs=87.1
Q ss_pred eeeeccCCC------CCcceeeccccccccchhh--hcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHHh
Q psy14859 773 FISTDASDL------GWGSQVDSSFLSGLWSREQ--QNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLRR 844 (1097)
Q Consensus 773 ~L~TDAS~~------GiGAVL~qa~~Sr~ls~aE--~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~~ 844 (1097)
.++||||.. |+|+++.+......+.... ..++..+.|+.|++.|++... .+...++.|+||++.++..+++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~-~~~~~~i~i~~Ds~~~~~~~~~ 79 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELAL-ELGGKKVNIYTDSQYVINALTG 79 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHH-hCCCceEEEEECHHHHHHHhhc
Confidence 378999987 8888888743222222222 468899999999999999755 5677899999999999999987
Q ss_pred cCCCCchhhHHHHHHHHHHhhccCceEEEEEecC----CCccccccccCC
Q psy14859 845 QGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPG----AYNSVADSLSRS 890 (1097)
Q Consensus 845 ~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipG----k~N~~ADaLSR~ 890 (1097)
...........+.+.+..++.+ ...+++.|+|| ..|..||.|+|.
T Consensus 80 ~~~~~~~~~~~~~~~i~~~~~~-~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 80 WYEGKPVKNVDLWQRLLALLKR-FHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred cccCCChhhHHHHHHHHHHHhC-CCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 6543344555666666666634 34678899999 999999999874
No 14
>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).
Probab=98.60 E-value=6.9e-08 Score=104.13 Aligned_cols=127 Identities=21% Similarity=0.263 Sum_probs=94.8
Q ss_pred ccCCceeEEeccccccccccccccccc---------ccccc---------ccc-ceEEeeccCccCCCChHHHHHhhHHH
Q psy14859 542 LQKGDYMISIDLSQAYFHVPIKTTHQR---------FLALS---------YNG-DVLAMTCLPFGLATAPQAFASLSNWV 602 (1097)
Q Consensus 542 L~~~~~fs~lDLksAY~qI~L~~edr~---------~taF~---------t~~-g~y~~~rLPFGL~nSP~~Fqr~m~~i 602 (1097)
..+..++.++|++++|..|.-+---+. ...+. ... ....-..+|+|...||.+|.-++..+
T Consensus 66 ~~~~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~GlpqG~~lSp~L~~~~l~~l 145 (226)
T cd01651 66 KGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQGGVISPLLANIYLHEL 145 (226)
T ss_pred cCCCeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceEccCCeEeCCCCCcCCCccHHHHHHHHHHHHH
Confidence 345689999999999998853211110 00000 011 12234569999999999999998887
Q ss_pred Hhhhhc-------------cCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCCC--CCeEEEeeEE
Q psy14859 603 ASLLRS-------------RGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLSP--APVLQFLGIM 667 (1097)
Q Consensus 603 l~~lr~-------------~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~p--~~~v~fLG~i 667 (1097)
...+.. .+.....|+||+++++.+.++....+..+...++..|+.+|++|+.+.. ...+.||||.
T Consensus 146 d~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~~~~~~fLG~~ 225 (226)
T cd01651 146 DKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFKSEGFDFLGFT 225 (226)
T ss_pred HHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHHHHcCCeechhhcceeecCCCCCeeCCeE
Confidence 766543 4457889999999999999888888888888999999999999998774 4689999986
Q ss_pred e
Q psy14859 668 W 668 (1097)
Q Consensus 668 I 668 (1097)
+
T Consensus 226 ~ 226 (226)
T cd01651 226 F 226 (226)
T ss_pred C
Confidence 4
No 15
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.44 E-value=3.4e-07 Score=90.77 Aligned_cols=116 Identities=19% Similarity=0.190 Sum_probs=84.0
Q ss_pred eeeeeccCCC------CCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHHhc
Q psy14859 772 HFISTDASDL------GWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLRRQ 845 (1097)
Q Consensus 772 ~~L~TDAS~~------GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~~~ 845 (1097)
+.|+||||.. |+|+|+........++......+.++.|+.|++.||+... -+...++.|+||++.++..+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~-~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCT-EHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHH-hCCCCEEEEEechHHHHHHHhHH
Confidence 5689998764 6788875432221222223346789999999999999643 33446899999999999999885
Q ss_pred CCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCccccccccCC
Q psy14859 846 GGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNSVADSLSRS 890 (1097)
Q Consensus 846 ~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~~ADaLSR~ 890 (1097)
.. +...+..+++.+..++.+|. .+.+.|+|+..|..||.|+|.
T Consensus 81 ~~-~~~~~~~l~~~~~~l~~~f~-~~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 81 YA-KNKMFAPLLEEALQYIKSFD-LFFIKWIPSSQNKVADELARK 123 (128)
T ss_pred Hh-cChhHHHHHHHHHHHHhcCC-ceEEEEcCchhchhHHHHHHH
Confidence 42 33345666777777777776 456799999999999999875
No 16
>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.
Probab=98.40 E-value=2.4e-07 Score=95.29 Aligned_cols=93 Identities=28% Similarity=0.334 Sum_probs=80.7
Q ss_pred EEeeccCccCCCChHHHHHhhHHHHhhhhc--cCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC
Q psy14859 579 LAMTCLPFGLATAPQAFASLSNWVASLLRS--RGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS 656 (1097)
Q Consensus 579 y~~~rLPFGL~nSP~~Fqr~m~~il~~lr~--~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~ 656 (1097)
.....+|+|...||.++..+|..+-..+.. .+.....|+||+++.+++.+.....+..+-+.+++.|+.+|++|+...
T Consensus 49 ~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~~ 128 (158)
T cd01646 49 GQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEIL 128 (158)
T ss_pred CCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEChhhceee
Confidence 345689999999999999999988777765 467899999999999999988888888999999999999999999877
Q ss_pred CCCe----EEEeeEEeCCC
Q psy14859 657 PAPV----LQFLGIMWDPH 671 (1097)
Q Consensus 657 p~~~----v~fLG~iIs~~ 671 (1097)
...+ .+|||+.+...
T Consensus 129 ~~~~~~~~~~flg~~~~~~ 147 (158)
T cd01646 129 PLPEGTASKDFLGYRFSPI 147 (158)
T ss_pred ecCCCCccccccceEeehh
Confidence 4544 69999999753
No 17
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=98.31 E-value=3.8e-07 Score=90.17 Aligned_cols=112 Identities=25% Similarity=0.229 Sum_probs=74.4
Q ss_pred cceeeeeccCC------CCCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHH
Q psy14859 770 VQHFISTDASD------LGWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLR 843 (1097)
Q Consensus 770 ~p~~L~TDAS~------~GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~ 843 (1097)
+.+++|||||- .|+|.|+... +.++..-...++++.||.|+..||+.+ ...+++|+||++.++..++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~---~~~~~~~~~~s~~~aEl~Ai~~AL~~~----~~~~v~I~tDS~~v~~~l~ 74 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGG---RNFSFRLGGQSNNRAELQAIIEALKAL----EHRKVTIYTDSQYVLNALN 74 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETT---EEEEEEEESECHHHHHHHHHHHHHHTH----STSEEEEEES-HHHHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECC---eEEEecccccchhhhheehHHHHHHHh----hcccccccccHHHHHHHHH
Confidence 46789999993 3666655332 233322227789999999999999954 3389999999999998777
Q ss_pred h----cCCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCcc-----ccccccC
Q psy14859 844 R----QGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNS-----VADSLSR 889 (1097)
Q Consensus 844 ~----~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~-----~ADaLSR 889 (1097)
+ .+.........+..+++..+.+ +..+.+.||||..|. .||.|+|
T Consensus 75 ~~~~~~~~~~~~~~~~i~~~i~~~~~~-~~~v~~~~V~~H~~~~~~N~~aD~lAk 128 (132)
T PF00075_consen 75 KWLHGNGWKKTSNGRPIKNEIWELLSR-GIKVRFRWVPGHSGVPQGNERADRLAK 128 (132)
T ss_dssp THHHHTTSBSCTSSSBHTHHHHHHHHH-SSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred Hhccccccccccccccchhheeecccc-ceEEeeeeccCcCCCchhHHHHHHHHH
Confidence 6 1111111111234456666643 667889999999654 6888876
No 18
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.20 E-value=3.1e-06 Score=85.91 Aligned_cols=119 Identities=24% Similarity=0.206 Sum_probs=84.0
Q ss_pred cceeeeeccCCC------CCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHH
Q psy14859 770 VQHFISTDASDL------GWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLR 843 (1097)
Q Consensus 770 ~p~~L~TDAS~~------GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~ 843 (1097)
..+.||||++.. |+|+||.-.-..+.++..+..-+.++.|+.|++.||+..+. +.-+.+.|+|||+-++..++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHH
Confidence 457899999864 67888884333344666666788899999999999997665 56678999999999987665
Q ss_pred hc----C-------CCCchhhHHHHHHHHHHhhccCceEEEEEecCC----CccccccccCC
Q psy14859 844 RQ----G-------GTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGA----YNSVADSLSRS 890 (1097)
Q Consensus 844 ~~----~-------~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk----~N~~ADaLSR~ 890 (1097)
.- + ..+......+.+++.+.+.++. .+.++||+|. .|..||.|.|.
T Consensus 81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~-~v~~~WVkgH~g~~~NeraD~LA~~ 141 (154)
T COG0328 81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHE-LVFWEWVKGHAGHPENERADQLARE 141 (154)
T ss_pred HHHhhccccCccccccCccccHHHHHHHHHHHhhCC-eEEEEEeeCCCCChHHHHHHHHHHH
Confidence 21 0 0011112245666667777763 4667999965 57788998885
No 19
>PRK07708 hypothetical protein; Validated
Probab=98.19 E-value=2.2e-06 Score=92.74 Aligned_cols=121 Identities=17% Similarity=0.043 Sum_probs=89.9
Q ss_pred cceeeeeccCC------CCCcceeeccccccc--cc---hhhhcccchHHhhhhHHHHHHHhhhhhc-cCceEeecCcHH
Q psy14859 770 VQHFISTDASD------LGWGSQVDSSFLSGL--WS---REQQNWHINKKEMFAVHQALSLNLPLLQ-SSVVMVQSDNQT 837 (1097)
Q Consensus 770 ~p~~L~TDAS~------~GiGAVL~qa~~Sr~--ls---~aE~~ysi~ekELlAIv~AL~~~r~~L~-g~~~~V~TDhk~ 837 (1097)
..+++|+|+|. .|+|+|+........ +. .-....+.++.|+.|++.||+.....=. ..++.|++|++.
T Consensus 72 ~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSql 151 (219)
T PRK07708 72 HEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQV 151 (219)
T ss_pred CcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHH
Confidence 35899999976 367778764211111 11 1111347889999999999996543211 124899999999
Q ss_pred HHHHHHhcCCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCccccccccCC
Q psy14859 838 VVSYLRRQGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNSVADSLSRS 890 (1097)
Q Consensus 838 lv~~l~~~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~~ADaLSR~ 890 (1097)
++.++++....+.+.+..+..++...+.++.+.+++.|||.+.|..||.|++.
T Consensus 152 Vi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~ 204 (219)
T PRK07708 152 VLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQ 204 (219)
T ss_pred HHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHH
Confidence 99999987777777777778888888888887788899999999999999986
No 20
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.01 E-value=9e-06 Score=95.26 Aligned_cols=118 Identities=19% Similarity=0.167 Sum_probs=89.3
Q ss_pred ceeeeeccCCC------CCcceeeccccc---cccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHH
Q psy14859 771 QHFISTDASDL------GWGSQVDSSFLS---GLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSY 841 (1097)
Q Consensus 771 p~~L~TDAS~~------GiGAVL~qa~~S---r~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~ 841 (1097)
.++|+||+|.. |+|+++...... ..+.......+.+..|+.|++.||+... -+..++++|++|++.++..
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~-~~g~~~v~i~~DS~lvi~~ 80 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAA-ELGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHH-hCCCCeEEEEeCcHHHHHH
Confidence 36799999875 677777653211 1122233356778999999999999543 3456789999999999999
Q ss_pred HHhcCCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCccccccccCC
Q psy14859 842 LRRQGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNSVADSLSRS 890 (1097)
Q Consensus 842 l~~~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~~ADaLSR~ 890 (1097)
+++....+...+..++.++..++.+|. .+++.|+|+..|..||.|++.
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~-~~~i~~v~r~~N~~AD~LA~~ 128 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFG-RVTYTWIPRARNAHADRLANE 128 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCC-ceEEEECCchhhhHHHHHHHH
Confidence 987655566667777777777888875 578899999999999999996
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.97 E-value=9.6e-06 Score=73.94 Aligned_cols=82 Identities=28% Similarity=0.344 Sum_probs=63.2
Q ss_pred hHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHHhcCCCCchhhHHHHHHHHHHhhccCceEEEEEecCCCccccc
Q psy14859 806 NKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLRRQGGTKSLSLLSEVEKIFLLSQDWRIHILAQFIPGAYNSVAD 885 (1097)
Q Consensus 806 ~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~~~~~~~~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~N~~AD 885 (1097)
.+.|++|+..||+.. .-+.-+++.+.||++.++..+++...... .+..++..+..++..|. .+.+.|+++..|..||
T Consensus 2 ~~aE~~al~~al~~a-~~~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~-~~~~~~i~r~~N~~A~ 78 (87)
T PF13456_consen 2 LEAEALALLEALQLA-WELGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFW-NVSVSHIPREQNKVAD 78 (87)
T ss_dssp HHHHHHHHHHHHHHH-HCCT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCS-CEEEEE--GGGSHHHH
T ss_pred cHHHHHHHHHHHHHH-HHCCCCEEEEEecCccccccccccccccc-cccccchhhhhhhcccc-ceEEEEEChHHhHHHH
Confidence 468999999999954 34556799999999999999988755555 67788888888888875 5788999999999999
Q ss_pred cccCC
Q psy14859 886 SLSRS 890 (1097)
Q Consensus 886 aLSR~ 890 (1097)
.|+|.
T Consensus 79 ~LA~~ 83 (87)
T PF13456_consen 79 ALAKF 83 (87)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 99874
No 22
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.96 E-value=1.1e-05 Score=82.49 Aligned_cols=115 Identities=21% Similarity=0.183 Sum_probs=73.1
Q ss_pred ceeeeeccCCC------CCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHHh
Q psy14859 771 QHFISTDASDL------GWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLRR 844 (1097)
Q Consensus 771 p~~L~TDAS~~------GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~~ 844 (1097)
.+.||||+|.. |+|+|+...-....++..+...+.++.||.|++.||+... ....+.|+||++.++..+++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~---~~~~v~I~tDS~yvi~~i~~ 79 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALK---EPCEVTLYTDSQYVRQGITE 79 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcC---CCCeEEEEECHHHHHHHHHH
Confidence 37899999973 5666665311111223333456778999999999998543 34679999999888765553
Q ss_pred ---------cCCCC--chhhHHHHHHHHHHhhccCceEEEEEecCCC----ccccccccCC
Q psy14859 845 ---------QGGTK--SLSLLSEVEKIFLLSQDWRIHILAQFIPGAY----NSVADSLSRS 890 (1097)
Q Consensus 845 ---------~~~~~--~~~l~~~~~r~~~~L~~f~~~i~I~hipGk~----N~~ADaLSR~ 890 (1097)
..... ......+..++..++... .+.+.||||.. |..||.|+|.
T Consensus 80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~--~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRH--QIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred HHHHHHHcCCcccCCCccccHHHHHHHHHHhccC--ceEEEEecCCCCCHHHHHHHHHHHH
Confidence 00111 111223445555555553 46779999776 7889998874
No 23
>PRK06548 ribonuclease H; Provisional
Probab=97.89 E-value=3e-05 Score=79.94 Aligned_cols=114 Identities=24% Similarity=0.241 Sum_probs=76.8
Q ss_pred cceeeeeccCCC------CCcceeeccccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHHHHHHH
Q psy14859 770 VQHFISTDASDL------GWGSQVDSSFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTVVSYLR 843 (1097)
Q Consensus 770 ~p~~L~TDAS~~------GiGAVL~qa~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~lv~~l~ 843 (1097)
..++||||+|.. |+|+++... ...+..+..-+.++.||.|++.||+.... .+.+++|+|||+.++..++
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~---~~~~g~~~~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~ 78 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDEN---TWDSGGWDIATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLT 78 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCC---cEEccCCCCCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHH
Confidence 458999998775 455555421 12333444567889999999999974331 2357999999999988777
Q ss_pred h-------cC---CCCch-hhHHHHHHHHHHhhccCceEEEEEecCCC----ccccccccCC
Q psy14859 844 R-------QG---GTKSL-SLLSEVEKIFLLSQDWRIHILAQFIPGAY----NSVADSLSRS 890 (1097)
Q Consensus 844 ~-------~~---~~~~~-~l~~~~~r~~~~L~~f~~~i~I~hipGk~----N~~ADaLSR~ 890 (1097)
+ .. ....+ ....+++.+..++++.. +++.||+|.. |..||.|.|.
T Consensus 79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~--v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRN--IRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCc--eEEEEEecCCCCHHHHHHHHHHHH
Confidence 3 11 11111 22355666666676654 6779999976 8889999886
No 24
>PRK08719 ribonuclease H; Reviewed
Probab=97.52 E-value=0.00014 Score=74.25 Aligned_cols=113 Identities=16% Similarity=0.066 Sum_probs=70.0
Q ss_pred cceeeeeccCCC---------CCcceeeccc----cccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcH
Q psy14859 770 VQHFISTDASDL---------GWGSQVDSSF----LSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQ 836 (1097)
Q Consensus 770 ~p~~L~TDAS~~---------GiGAVL~qa~----~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk 836 (1097)
.++++|||+|.. |+|+++...- ...... .+...+.++.||.|++.||+.... ..+|+||++
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~-~~~~~Tnn~aEl~A~~~aL~~~~~-----~~~i~tDS~ 76 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSIT-VNRYTDNAELELLALIEALEYARD-----GDVIYSDSD 76 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEec-CCCCccHHHHHHHHHHHHHHHcCC-----CCEEEechH
Confidence 468899998872 6677765421 011111 122357899999999999986432 248999998
Q ss_pred HHHHHHHh-------cC-CCC--ch-hhHHHHHHHHHHhhccCceEEEEEecC----CCccccccccCC
Q psy14859 837 TVVSYLRR-------QG-GTK--SL-SLLSEVEKIFLLSQDWRIHILAQFIPG----AYNSVADSLSRS 890 (1097)
Q Consensus 837 ~lv~~l~~-------~~-~~~--~~-~l~~~~~r~~~~L~~f~~~i~I~hipG----k~N~~ADaLSR~ 890 (1097)
.++..+++ .. .+. .+ ....+.+.+..+.++. .++++|||| ..|..||.|.|.
T Consensus 77 yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~--~i~~~~VkgH~g~~~Ne~aD~lA~~ 143 (147)
T PRK08719 77 YCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARK--YVEVEKVTAHSGIEGNEAADMLAQA 143 (147)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCC--cEEEEEecCCCCChhHHHHHHHHHH
Confidence 88766642 11 111 11 1123344444444433 477799999 558899998874
No 25
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=97.31 E-value=0.0002 Score=73.92 Aligned_cols=115 Identities=20% Similarity=0.227 Sum_probs=71.6
Q ss_pred hhhhhhhccccccccccCCccchhhhHHHHHHhhcCCCCCC-CCCcccchhhHHhhhhCCCCCC-----CCC----CCcc
Q psy14859 702 SARSLLGYLSFASFVIPMGRLHSRRIQRQASLLRLGAPHLT-PINPAVLPKLEWWLNALPLSSP-----IFP----RQVQ 771 (1097)
Q Consensus 702 eLrsfLGllny~r~fI~~~~~~arpL~~ll~~lkk~~~~W~-~~~q~Af~~LK~~l~~l~~~~P-----il~----~~~p 771 (1097)
.+.++..-+|++..++-.++.+. ..+-+.+..|| +..++....+..|.+++....+ .+. ....
T Consensus 9 ~ia~~yDPlGl~~p~~i~~K~ll-------q~lw~~~l~WD~~lp~el~~~w~~~~~~l~~~~~i~iPR~i~~~~~~~~~ 81 (159)
T PF05380_consen 9 FIASIYDPLGLLAPIIIRAKLLL-------QKLWQSKLDWDDPLPDELRKEWKKWLKELESLSPIRIPRCIPISDYRSVE 81 (159)
T ss_pred HHHHHcCcchhhHHHHHHHHHHH-------HhhhccccchhhhhhHHHHHHHHHHHHHHhhcccccCCccccccccccee
Confidence 34455555555554443332222 22345668999 5677777777778776543222 112 1356
Q ss_pred eeeeeccCCCCCcceeeccc-----------cccccchhhhcccchHHhhhhHHHHHHHhhhh
Q psy14859 772 HFISTDASDLGWGSQVDSSF-----------LSGLWSREQQNWHINKKEMFAVHQALSLNLPL 823 (1097)
Q Consensus 772 ~~L~TDAS~~GiGAVL~qa~-----------~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~ 823 (1097)
+++|+|||..|+|||++-.+ +++.--..-+..+|.++||+|++.+++-....
T Consensus 82 L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 82 LHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV 144 (159)
T ss_pred eeEeecccccceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999987643 12221122345599999999999999854443
No 26
>KOG3752|consensus
Probab=96.53 E-value=0.0066 Score=69.30 Aligned_cols=118 Identities=19% Similarity=0.224 Sum_probs=76.5
Q ss_pred ceeeeeccCCCC---------Ccceeec---cccccccchhhhcccchHHhhhhHHHHHHHhhhhhccCceEeecCcHHH
Q psy14859 771 QHFISTDASDLG---------WGSQVDS---SFLSGLWSREQQNWHINKKEMFAVHQALSLNLPLLQSSVVMVQSDNQTV 838 (1097)
Q Consensus 771 p~~L~TDAS~~G---------iGAVL~q---a~~Sr~ls~aE~~ysi~ekELlAIv~AL~~~r~~L~g~~~~V~TDhk~l 838 (1097)
..+||||+|..| +|..+.. ...|+.+. -..-+.++.||.||..||++.+.- ...+++|.||+..+
T Consensus 212 ~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~--~g~qtNnrAEl~Av~~ALkka~~~-~~~kv~I~TDS~~~ 288 (371)
T KOG3752|consen 212 IQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLA--GGRQTNNRAELIAAIEALKKARSK-NINKVVIRTDSEYF 288 (371)
T ss_pred ceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCC--CCcccccHHHHHHHHHHHHHHHhc-CCCcEEEEechHHH
Confidence 378999998765 3333332 12222222 123467899999999999985442 33499999999999
Q ss_pred HHHHHhc---------CCCCchh-------hHHHHHHHHHHhhc-cCceEEEEEecCCC----ccccccccCCC
Q psy14859 839 VSYLRRQ---------GGTKSLS-------LLSEVEKIFLLSQD-WRIHILAQFIPGAY----NSVADSLSRSK 891 (1097)
Q Consensus 839 v~~l~~~---------~~~~~~~-------l~~~~~r~~~~L~~-f~~~i~I~hipGk~----N~~ADaLSR~~ 891 (1097)
+.+|+.. .+..... .......+.++.++ -+..+++.||+|.. |..||+|+|..
T Consensus 289 i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 289 INSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred HHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 8877640 1111111 11234455566666 35678889999975 77899999973
No 27
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). 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.
Probab=95.69 E-value=0.046 Score=62.59 Aligned_cols=125 Identities=14% Similarity=0.095 Sum_probs=83.9
Q ss_pred eeccCccCCCChHHHHHhhHHHHhhhhc--cCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC--
Q psy14859 581 MTCLPFGLATAPQAFASLSNWVASLLRS--RGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS-- 656 (1097)
Q Consensus 581 ~~rLPFGL~nSP~~Fqr~m~~il~~lr~--~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~-- 656 (1097)
-+.+|+|-..||.+-.-.|...-..+.. .|...+.|.||+++++. .+++......+-+.++..|+.+|++|....
T Consensus 81 ~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~-~~~a~~aw~~i~~fl~~lGLelN~eKT~iV~~ 159 (346)
T cd01709 81 KRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ-PETCAKAWKAIQEFAKVMGLELNKEKTGSVYL 159 (346)
T ss_pred CCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC-HHHHHHHHHHHHHHHHHcCceeccccceEEEe
Confidence 3679999999999877777633333332 37789999999999955 678888888899999999999999885432
Q ss_pred ---------------CCCeEEEeeEEeCCCCCcccCcchhhhh-hhHHHHHhhhccccChhhhhhhhhccc
Q psy14859 657 ---------------PAPVLQFLGIMWDPHLDRMWLPEDKQLT-LGNILRTLLASKTWNLDSARSLLGYLS 711 (1097)
Q Consensus 657 ---------------p~~~v~fLG~iIs~~gi~v~l~~~Ki~a-i~~~~~il~~~~P~t~keLrsfLGlln 711 (1097)
|...++|-=..+++...+..+|.++++. +.++...+ . ..+.+-+++..-|
T Consensus 160 ~~~~r~~~~~~~~~LP~g~i~wgfL~Ld~~~G~~~Idq~~Vd~hi~el~~QL-~----~c~Sv~~wiq~WN 225 (346)
T cd01709 160 SDDTKTRDTTIDATLPEGPVRWGFLKLDPKTGRWEIDQSQVDAHIDELRKQL-D----ACKSVLSWIQAWN 225 (346)
T ss_pred ccCCccCCCcccccCCCCCceeeeEEecCCCCcEEeeHHHHHHHHHHHHHHh-h----cCchHHHHHHHHH
Confidence 2333444434455543333458888876 44444333 1 1245556666666
No 28
>PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 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. This entry includes reverse transcriptases not recognised by IPR000477 from INTERPRO [].
Probab=94.28 E-value=0.022 Score=63.21 Aligned_cols=126 Identities=18% Similarity=0.256 Sum_probs=79.9
Q ss_pred CceeEEeccccccccccccccc--ccccccccc---cceEEeeccCccCCCChHHHHHhhHHHHhhhh------------
Q psy14859 545 GDYMISIDLSQAYFHVPIKTTH--QRFLALSYN---GDVLAMTCLPFGLATAPQAFASLSNWVASLLR------------ 607 (1097)
Q Consensus 545 ~~~fs~lDLksAY~qI~L~~ed--r~~taF~t~---~g~y~~~rLPFGL~nSP~~Fqr~m~~il~~lr------------ 607 (1097)
.-.+-.+|++.||.+-.|+++- +.-.+|..+ +..+...+--+||+.||..|...++..|..+.
T Consensus 76 ~~~~~q~Dv~tAfL~~~l~e~iym~~P~g~~~~~~~~~v~~L~kaLYGLKQa~r~W~~~l~~~L~~~GF~~~~~D~clfi 155 (246)
T PF07727_consen 76 GLELHQMDVKTAFLNGDLDEEIYMRQPPGFEDPGPPGKVCRLKKALYGLKQAPRLWYKTLDKFLKKLGFKQSKADPCLFI 155 (246)
T ss_pred ccccccccccceeeecccccchhhcccccccccccccccccccccceecccccchhhhhcccccchhhhhcccccccccc
Confidence 4457789999999999988762 123345444 34677778889999999999888887776432
Q ss_pred ----ccCceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCCCCCeEEEeeEEeCCCCCcccCcchh
Q psy14859 608 ----SRGMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLSPAPVLQFLGIMWDPHLDRMWLPEDK 681 (1097)
Q Consensus 608 ----~~g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~p~~~v~fLG~iIs~~gi~v~l~~~K 681 (1097)
+....+.+||||++|.+.+.+.... +.+.|. ..|.++. . ..--.|||..|......+.+...+
T Consensus 156 ~~~~~~~~ii~vYVDDili~~~~~~~i~~----~~~~l~-~~F~iKd----l--G~~~~fLGi~i~~~~~~i~lsQ~~ 222 (246)
T PF07727_consen 156 KKSGDGFIIILVYVDDILIAGPSEEEIEE----FKKELK-KKFEIKD----L--GELKYFLGIEIERTKGGIFLSQKA 222 (246)
T ss_pred cccccccccccccccccccccccccceec----cccccc-ccccccc----c--cccccccceEEEECCCEEEEcHHH
Confidence 0123567999999999998754432 222222 1222221 1 122358999886544444444433
No 29
>KOG4768|consensus
Probab=91.55 E-value=0.24 Score=59.61 Aligned_cols=137 Identities=17% Similarity=0.231 Sum_probs=96.9
Q ss_pred cccccccccCCceeEEecccccccccccccc---------cccc---------cccccccc--eEEeeccCccCCCChHH
Q psy14859 535 HFRIPSFLQKGDYMISIDLSQAYFHVPIKTT---------HQRF---------LALSYNGD--VLAMTCLPFGLATAPQA 594 (1097)
Q Consensus 535 i~~ll~~L~~~~~fs~lDLksAY~qI~L~~e---------dr~~---------taF~t~~g--~y~~~rLPFGL~nSP~~ 594 (1097)
+-++...++++.||...||++.|-.|+-++- |..+ .+..+..+ ++++...|+|-..||.+
T Consensus 349 i~~~~n~f~gcnw~ie~DLkkcfdtIphd~LI~eL~~rIkdk~fidL~~kll~AGy~ten~ry~~~~lGtpqgsvvspil 428 (796)
T KOG4768|consen 349 ILKTHNLFRGCNWFIEVDLKKCFDTIPHDELIIELQKRIKDKGFIDLNYKLLRAGYTTENARYHVEFLGTPQGSVVSPIL 428 (796)
T ss_pred HHHHHHHhhccceEEechHHHHhccccHHHHHHHHHHHHhhhhHHHHHHHHHhcCccccccceecccccccccccCCchh
Confidence 3455667889999999999999999985442 1111 11223333 56788899999999988
Q ss_pred HHHhhHHHHhhhhc-----------------------------------------------------cC---ceEEEEec
Q psy14859 595 FASLSNWVASLLRS-----------------------------------------------------RG---MRVVVYLD 618 (1097)
Q Consensus 595 Fqr~m~~il~~lr~-----------------------------------------------------~g---~~v~vYvD 618 (1097)
-..+|+.+-..++. .| ..-+.|.|
T Consensus 429 ~nifL~~LDk~Lenk~~nefn~~~~~~~rhs~yr~L~~~iakaKl~s~~sKtirlrd~~qrn~~n~~~gfkr~~yVRyad 508 (796)
T KOG4768|consen 429 CNIFLRELDKRLENKHRNEFNAGHLRSARHSKYRNLSDSIAKAKLTSGMSKTIRLRDGVQRNETNDTAGFKRLMYVRYAD 508 (796)
T ss_pred HHHHHHHHHHHHHHHHHhhhcccCcccccChhhhhHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccceeeEEEecC
Confidence 76666554333220 00 02368999
Q ss_pred Cceeeec-CchhHHHhhhHHHHHHhhccceeccccCCCC-CCCeEEEeeEEeCCC
Q psy14859 619 DFLLVNQ-DPRILEIQGKLAVSILGSLGWIVNLQKSSLS-PAPVLQFLGIMWDPH 671 (1097)
Q Consensus 619 DILI~s~-s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~-p~~~v~fLG~iIs~~ 671 (1097)
|++|..- +..++.+.++.+-..+...|+..+++|.+.- ..+.+.|||+.|+..
T Consensus 509 d~ii~v~GS~nd~K~ilr~In~f~sslGls~n~~kt~it~S~eg~~flg~nis~t 563 (796)
T KOG4768|consen 509 DIIIGVWGSVNDCKQILRDINNFLSSLGLSNNSSKTQITVSREGTHFLGYNISTT 563 (796)
T ss_pred CEEEEEeccHHHHHHHHHHHHHHHHhhCcccCcccceEEeeccceeeeeceeccC
Confidence 9988754 7788888888888899999999999997754 234478999998753
No 30
>cd06094 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified
Probab=88.42 E-value=0.42 Score=44.49 Aligned_cols=73 Identities=19% Similarity=0.017 Sum_probs=48.8
Q ss_pred eeccccccchhhhccchhhhhhcccCCCCcccccccceeeeeecCc---------ceecccccccccC-----CCCCccc
Q psy14859 303 RRAFSSTMNTLVEKYPEVREELGSLFSDESVFKNVSDHLLQYVCGK---------RAECLESRRRLVE-----PRDPHLA 368 (1097)
Q Consensus 303 ~~~~~~~~~~~~~~~~~~~~el~n~~~~~~p~~~~~~~~l~~~~g~---------~~~C~~~~~~~~~-----~~~~~il 368 (1097)
++...|++++++|+++.++-.=.+..... ..-+...+..++|. ...+.+.+|.+.| +....|+
T Consensus 3 v~D~~s~~~fLVDTGA~vSviP~~~~~~~---~~~~~~~l~AANgt~I~tyG~~~l~ldlGlrr~~~w~FvvAdv~~pIl 79 (89)
T cd06094 3 VRDRTSGLRFLVDTGAAVSVLPASSTKKS---LKPSPLTLQAANGTPIATYGTRSLTLDLGLRRPFAWNFVVADVPHPIL 79 (89)
T ss_pred eEECCCCcEEEEeCCCceEeecccccccc---ccCCceEEEeCCCCeEeeeeeEEEEEEcCCCcEEeEEEEEcCCCccee
Confidence 45667899999999987743333222110 12233355555554 3666788878877 7788999
Q ss_pred chHHHHhcCC
Q psy14859 369 SLLLRARRGK 378 (1097)
Q Consensus 369 G~d~l~~~g~ 378 (1097)
|.|++++++.
T Consensus 80 GaDfL~~~~l 89 (89)
T cd06094 80 GADFLQHYGL 89 (89)
T ss_pred cHHHHHHcCC
Confidence 9999999874
No 31
>PF02160 Peptidase_A3: Cauliflower mosaic virus peptidase (A3); InterPro: IPR000588 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of sequences contain an aspartic peptidase signature that belongs to MEROPS peptidase family A3, subfamily A3A (cauliflower mosaic virus-type endopeptidase, clan AA). Cauliflower mosaic virus belongs to the Retro-transcribing viruses, which have a double-stranded DNA genome. The genome includes an open reading frame (ORF V) that shows similarities to the pol gene of retroviruses. This ORF codes for a polyprotein that includes a reverse transcriptase, which, on the basis of a DTG triplet near the N terminus, was suggested to include an aspartic protease. The presence of an aspartic protease has been confirmed by mutational studies, implicating Asp-45 in catalysis. The protease releases itself from the polyprotein and is involved in reactions required to process the ORF IV polyprotein, which includes the viral coat protein []. The viral aspartic peptidase signature has also been found associated with a polyprotein encoded by integrated pararetrovirus-like sequences in the genome of Nicotiana tabacum (Common tobacco) []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis
Probab=85.40 E-value=0.28 Score=52.32 Aligned_cols=55 Identities=16% Similarity=0.183 Sum_probs=49.1
Q ss_pred ccchhhhhhcccCCC-CcccccccceeeeeecC-cceecccccccccCCCCCcccch
Q psy14859 316 KYPEVREELGSLFSD-ESVFKNVSDHLLQYVCG-KRAECLESRRRLVEPRDPHLASL 370 (1097)
Q Consensus 316 ~~~~~~~el~n~~~~-~~p~~~~~~~~l~~~~g-~~~~C~~~~~~~~~~~~~~ilG~ 370 (1097)
.....+..||+||++ +.||.||.+.+.++..+ ..+++.++++++..+..+|++++
T Consensus 87 ~~~g~d~IlG~NF~r~y~Pfiq~~~~I~f~~~~~~~~~~~ki~ka~~~~~~~f~es~ 143 (201)
T PF02160_consen 87 QESGIDIILGNNFLRLYEPFIQTEDRIQFHKKGLQKVEIKKITKAIRKGKPGFLESM 143 (201)
T ss_pred ecCCCCEEecchHHHhcCCcEEEccEEEEEeCCcceeehhhhhhhhhccCccccHhH
Confidence 445568999999999 99999999999999998 58899999999999999998864
No 32
>cd01699 RNA_dep_RNAP RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.
Probab=70.16 E-value=8.6 Score=42.93 Aligned_cols=59 Identities=20% Similarity=0.208 Sum_probs=45.7
Q ss_pred CceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC---CCCeEEEeeEEeC
Q psy14859 610 GMRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS---PAPVLQFLGIMWD 669 (1097)
Q Consensus 610 g~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~---p~~~v~fLG~iIs 669 (1097)
...+++|=||.++..++. ........+.+.+.++|+.++..|.... +..+++|||+.+.
T Consensus 194 ~~~~~~~GDD~li~~~~~-~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~Fl~r~f~ 255 (278)
T cd01699 194 NVRLLNYGDDCLLSVEKA-DDKFNLETLAEWLKEYGLTMTDEDKVESPFRPLEEVEFLKRRFV 255 (278)
T ss_pred ceEEEEEcCCeEEEechh-HhhhCHHHHHHHHHHcCCEeCCcccCCCCCCCHhhCcccCCccE
Confidence 346889999999998865 3334455677888889999999997752 4778999997764
No 33
>PF06817 RVT_thumb: Reverse transcriptase thumb domain; InterPro: IPR010661 This domain is known as the thumb domain. It is composed of a four helix bundle []. Reverse transcriptase converts the viral RNA genome into double-stranded viral DNA. Reverse transcriptase often occurs in a polyprotein; with integrase, ribonuclease H and/or protease, which is cleaved before the enzyme takes action. The impact of antiretroviral treatment on the first 400 amino acids of HIV reverse transcriptase is good. Little is known, however, of the antiretroviral drug impact on the C-terminal domains of Pol, which includes the thumb, connection and RNase H []. Evidence suggests that these might be well conserved domains.; GO: 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 2JLE_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B 1FK9_B 3DM2_B 1JLQ_B 3LAM_A ....
Probab=63.34 E-value=1.3 Score=39.58 Aligned_cols=34 Identities=24% Similarity=0.498 Sum_probs=26.8
Q ss_pred cccChhhhhhhhhccccccccccCCccchhhhHHHH
Q psy14859 696 KTWNLDSARSLLGYLSFASFVIPMGRLHSRRIQRQA 731 (1097)
Q Consensus 696 ~P~t~keLrsfLGllny~r~fI~~~~~~arpL~~ll 731 (1097)
..+|+.++|+++|.+||.+..+++. ..++|++++
T Consensus 13 ~~~TlndiQKLvG~lnW~sqi~~gi--~~k~L~kll 46 (70)
T PF06817_consen 13 ESWTLNDIQKLVGKLNWASQIYPGI--KLKQLCKLL 46 (70)
T ss_dssp SSEBHHHHHHHHHHHHHHTCTSTTS---THHHHHCT
T ss_pred CchhHHHHHHHHhheeeeeeeecCc--chhHHHHHh
Confidence 4789999999999999999777764 366666654
No 34
>KOG1005|consensus
Probab=59.39 E-value=18 Score=46.17 Aligned_cols=77 Identities=16% Similarity=0.174 Sum_probs=61.0
Q ss_pred EeeccCccCCCChHHHHHhhHHHHhh----hhccCc-eEEEEecCceeeecCchhHHHhhhHHHHHHhhccceecccc-C
Q psy14859 580 AMTCLPFGLATAPQAFASLSNWVASL----LRSRGM-RVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQK-S 653 (1097)
Q Consensus 580 ~~~rLPFGL~nSP~~Fqr~m~~il~~----lr~~g~-~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~K-c 653 (1097)
+-..+|+|-.-|..+-.-.+..+.+. ..+.|. .++.|+||.|+.+.+.++...-++.+..-..++|+..|.+| |
T Consensus 631 q~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a~kfl~~l~~Gf~~yn~~tn~~K~~ 710 (888)
T KOG1005|consen 631 QKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQAKKFLKLLSRGFNKYNFFTNEPKTV 710 (888)
T ss_pred EecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHHHHHHHHHhccccccceeccCcccc
Confidence 45678999998888776666665553 334454 67799999999999999999888888888999999999999 4
Q ss_pred CCC
Q psy14859 654 SLS 656 (1097)
Q Consensus 654 ~f~ 656 (1097)
.|.
T Consensus 711 nF~ 713 (888)
T KOG1005|consen 711 NFE 713 (888)
T ss_pred ccc
Confidence 443
No 35
>KOG0307|consensus
Probab=43.13 E-value=1.3e+02 Score=39.68 Aligned_cols=119 Identities=24% Similarity=0.343 Sum_probs=66.3
Q ss_pred CCceeeccCCCccceecccCCCCCCCCCCCCccchhhhhcCccccCCCCCCcccccCCCccccCCCCcchhHHHHhhhcc
Q psy14859 90 PSATVQAAPGSSASVLAAPLPSSSGQPFISPPAQSAAFLAQPASTASLPPSAAHHLYPLPFFCDPSYYGHYLQSAMKASR 169 (1097)
Q Consensus 90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (1097)
+|-.+..-|+.+.++.-+|-.-..|.-+..||++....-.-+-.++..|+..+-+. .+ .|+ +..|. ..
T Consensus 837 ~S~p~~~~pv~sgs~~P~~~~~~p~~~~~~~p~~~g~~~~~~iP~~~~P~a~~~~p---~~--~P~------~~~~s-v~ 904 (1049)
T KOG0307|consen 837 PSFPYAPNPVTSGSVNPAPYGPGPPGSWNQPPALQGSYRKPKIPPTVMPPAPITSP---NG--GPS------QNPQS-VQ 904 (1049)
T ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCCcccCCCcccCCCCCCCCCcccCCCccccCC---CC--CCC------CCccc-cc
Confidence 34444444566666766664455666677788877776666666666665442221 11 332 23344 33
Q ss_pred CccCCCCCCCCCCCceecCCCCCCcccccccCccccCCcccccccCCCCcCCCCCCCCCchhccccccc
Q psy14859 170 GQVAQPPPPSESVTPIPLSPVSSDQEDFSEEDEVVDCNPPALFSFAPSTKEREPSIPDPDSELASQGVV 238 (1097)
Q Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 238 (1097)
++..+++-+..++.++|..+ -|+-.--.+..+...+.|..|.+...+.++.
T Consensus 905 p~~P~~~~~~~~~s~~Ptp~------------------~~~~~~~Q~~~~~~~~~~~~P~~~~~i~~~~ 955 (1049)
T KOG0307|consen 905 PQSPPIPQPLPPVSPAPTPG------------------QPAPLQSQPLPTAPAPKHPIPEELQIIETFL 955 (1049)
T ss_pred CCCCCCCCCCCCCCCCCCCC------------------CCCCcccccCCCCCCcccCCchHHHHHHHHH
Confidence 33333333444444555111 1112223567778889999999999888876
No 36
>COG0313 Predicted methyltransferases [General function prediction only]
Probab=42.11 E-value=14 Score=41.40 Aligned_cols=66 Identities=32% Similarity=0.461 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHhcccCCC---CCCCCCCCCCccCCCCCCCCCCCCCCCCCccccccchhccCCCceeeccCCCccceecc
Q psy14859 31 RCLAQLVQAITARKSSTL---DQSPAVSDPGMASGVSDQSPPLSSAPANPVQASAPVQAAHQPSATVQAAPGSSASVLAA 107 (1097)
Q Consensus 31 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 107 (1097)
.++..|+..+...++-.| -.-|.+||||. .=|.+||.-.-.|..-||.||.+.|.
T Consensus 65 ~~~~~li~~l~~g~~valVSDAG~P~ISDPG~----------------------~LV~~a~~~gi~V~~lPG~sA~~tAL 122 (275)
T COG0313 65 EKLPKLIPLLKKGKSVALVSDAGTPLISDPGY----------------------ELVRAAREAGIRVVPLPGPSALITAL 122 (275)
T ss_pred HHHHHHHHHHhcCCeEEEEecCCCCcccCccH----------------------HHHHHHHHcCCcEEecCCccHHHHHH
Confidence 466777888877765443 12344444443 34788999999999999999988776
Q ss_pred cCCCCCCCCCC
Q psy14859 108 PLPSSSGQPFI 118 (1097)
Q Consensus 108 ~~~~~~~~~~~ 118 (1097)
-...-.+|+|+
T Consensus 123 ~~SGl~~~~F~ 133 (275)
T COG0313 123 SASGLPSQRFL 133 (275)
T ss_pred HHcCCCCCCee
Confidence 55555556664
No 37
>PF05919 Mitovir_RNA_pol: Mitovirus RNA-dependent RNA polymerase; InterPro: IPR008686 This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana [].
Probab=41.61 E-value=54 Score=39.81 Aligned_cols=152 Identities=25% Similarity=0.310 Sum_probs=87.4
Q ss_pred ceeEEEEecCCCCcccc--cccC------Cccccc--------CCccccccccccccccccCCceeEEeccccccccccc
Q psy14859 499 LSRLFLVPKGNGGTRPV--LNLK------GLNQFL--------SPKKFSLINHFRIPSFLQKGDYMISIDLSQAYFHVPI 562 (1097)
Q Consensus 499 ~SPv~~V~Kkdgk~R~v--vD~R------~LN~~t--------~~~~~plP~i~~ll~~L~~~~~fs~lDLksAY~qI~L 562 (1097)
..-+.+|+.+.||.|++ +||- .|.+.+ ....|.....-+.+....+.+.+..+||++|--..||
T Consensus 85 ~gkLs~~~d~~gK~Ri~Am~D~~tQ~~L~PlH~~lf~~Lr~ip~DgTF~Q~~~~~~~~~~~~~~~~~S~DLsaATDR~Pi 164 (498)
T PF05919_consen 85 LGKLSIKEDPEGKVRIFAMVDYWTQCVLKPLHDWLFSILRRIPQDGTFDQEPPFDRLVDSMKEKYFYSFDLSAATDRFPI 164 (498)
T ss_pred hcceEEeEcCCCceEEEEEEeHHHHHhhHHHHHHHHHHHhcCCCCCCcCCCCchhhHhhcccCCceEEEeeccccccccH
Confidence 45677788888999985 4654 222221 1122222211111111222233899999999888887
Q ss_pred cccccccc------------------cc-ccccceEEeec-cCccCCCChHHHHHhhHHHHhhh--hc-cCc---eEEEE
Q psy14859 563 KTTHQRFL------------------AL-SYNGDVLAMTC-LPFGLATAPQAFASLSNWVASLL--RS-RGM---RVVVY 616 (1097)
Q Consensus 563 ~~edr~~t------------------aF-~t~~g~y~~~r-LPFGL~nSP~~Fqr~m~~il~~l--r~-~g~---~v~vY 616 (1097)
.-+-+-.. .| ...++.++|.+ =|+|.-.|=+.|.-.=+-+++.. +. -+. .-.+-
T Consensus 165 ~lQ~~il~~l~~~~~a~~W~~llv~r~~~~~~~~~v~y~vGQPmGa~SSW~~~altHH~iV~~aA~~~~~~~~f~~Y~iL 244 (498)
T PF05919_consen 165 VLQERILSYLFGDSFASSWRSLLVGRPYLKPNGDEVRYSVGQPMGAYSSWAMFALTHHLIVQYAAERVGGGSRFTDYIIL 244 (498)
T ss_pred HHHHHHHHHHhCchHHHHHHHHHcCCccccCCCCeEEEecCCcchhccccHHHHhhHHHHHHHHHHHhhccCCCCceEEE
Confidence 64432211 11 22345566644 69999999888876666665521 11 011 12344
Q ss_pred ecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC
Q psy14859 617 LDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS 656 (1097)
Q Consensus 617 vDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~ 656 (1097)
=|||+|.-+.. .+.-...+..+|+.++..|+...
T Consensus 245 GDDivi~~~~v------A~~Y~~~m~~Lgv~is~~Ks~vS 278 (498)
T PF05919_consen 245 GDDIVIANDKV------AKQYLSIMTDLGVEISLSKSHVS 278 (498)
T ss_pred cCcEEEcCHHH------HHHHHHHHHHcCceeccCccccc
Confidence 58888876533 33345678889999999998764
No 38
>KOG1985|consensus
Probab=33.50 E-value=1.4e+02 Score=38.53 Aligned_cols=30 Identities=20% Similarity=0.365 Sum_probs=16.3
Q ss_pred CCCCCcccccccccccCCCCcceeEEEEee
Q psy14859 1018 SRPLTSLFITTRGIVQPASRSVIAGWVKTA 1047 (1097)
Q Consensus 1018 ~~~~~~~~i~~~g~~~~~~~~~~~~~v~~~ 1047 (1097)
..+++...+.-+|+|=--.++++.+||-..
T Consensus 762 ~L~ltae~l~~~GlyL~D~g~~lfl~vg~~ 791 (887)
T KOG1985|consen 762 PLNLTAELLSRRGLYLMDTGTTLFLWVGSN 791 (887)
T ss_pred ccchHHHHhccCceEEEecCcEEEEEEcCC
Confidence 344444445555555444456677777644
No 39
>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....
Probab=32.32 E-value=52 Score=40.27 Aligned_cols=58 Identities=22% Similarity=0.256 Sum_probs=45.3
Q ss_pred ceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceecc-ccCCC----CCCCeEEEeeEEeC
Q psy14859 611 MRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNL-QKSSL----SPAPVLQFLGIMWD 669 (1097)
Q Consensus 611 ~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~-~Kc~f----~p~~~v~fLG~iIs 669 (1097)
..+++|=||.++..+..-... ....+.+.+++.|+++.. +|..- .+-.+++||...+.
T Consensus 344 ~~~i~YGDD~l~sv~~~~~~~-n~~~i~~~~~~~G~~~T~~dK~~~~~~~~~~~~v~FLkR~f~ 406 (491)
T PF00680_consen 344 VKLIVYGDDNLISVPPEIDPW-NGETISEFLAELGLTYTDADKTGEFPPFRPLEEVSFLKRTFV 406 (491)
T ss_dssp SEEEEETTEEEEEESSHHHHH-HHHHHHHHHHTTTEEEEESSTSSSCSSBBCTTTHEETTEEEE
T ss_pred eeeeeeccccchhhhcccccc-hhHHHHHHHHhcccccccccccCCccccCcccccccccccee
Confidence 357899999999988665555 788889999999999987 66552 24578999986663
No 40
>KOG0162|consensus
Probab=30.43 E-value=1.1e+02 Score=38.55 Aligned_cols=13 Identities=31% Similarity=0.442 Sum_probs=5.4
Q ss_pred CccchhhhhcCcc
Q psy14859 120 PPAQSAAFLAQPA 132 (1097)
Q Consensus 120 ~~~~~~~~~~~~~ 132 (1097)
|+.++.....||+
T Consensus 990 p~~~s~~~s~~~~ 1002 (1106)
T KOG0162|consen 990 PVSTSTTTSQQPS 1002 (1106)
T ss_pred CCCcccccccccc
Confidence 4444443334443
No 41
>PHA00028 rep RNA replicase, beta subunit
Probab=28.96 E-value=78 Score=38.54 Aligned_cols=39 Identities=23% Similarity=0.427 Sum_probs=31.8
Q ss_pred ceEEEEecCceeeecCchhHHHhhhHHHHHHhhccceeccccCCCC
Q psy14859 611 MRVVVYLDDFLLVNQDPRILEIQGKLAVSILGSLGWIVNLQKSSLS 656 (1097)
Q Consensus 611 ~~v~vYvDDILI~s~s~eeh~~~l~~Vl~~L~~~Gl~ln~~Kc~f~ 656 (1097)
..|-+|=|||+|-++ ....+++.|.-.||..|.+|..+.
T Consensus 334 ~ti~VYGDDIIvps~-------~a~~li~vlsyvgF~pN~kKTF~~ 372 (561)
T PHA00028 334 GTISVYGDDIIVPTE-------VAPPLINVLSYVGFMPNLKKTFWT 372 (561)
T ss_pred CeeEEecCceEeehh-------hhHHHHHHHHHhceecCCcccccc
Confidence 378899999999765 345677888999999999997654
No 42
>KOG4525|consensus
Probab=21.05 E-value=71 Score=37.86 Aligned_cols=33 Identities=48% Similarity=0.467 Sum_probs=27.4
Q ss_pred CCchhhhhccchhhhhHHHHHHHHHHHHHHHhcc
Q psy14859 11 DPQPEAKRLCHLEEKTEKIERCLAQLVQAITARK 44 (1097)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 (1097)
|-+-|+|-+-.++|-..|| ||-|.|+|||||.|
T Consensus 112 d~p~e~K~~n~~~e~i~kl-rl~arL~Qa~tae~ 144 (614)
T KOG4525|consen 112 DCPDEEKTLNQQHEVISKL-RLNARLVQAITAEK 144 (614)
T ss_pred cCcchhcccchHHHHHHHH-HHHHHHHHHHHHHH
Confidence 5567888888888877776 89999999999976
Done!