Query psy15121
Match_columns 960
No_of_seqs 690 out of 3513
Neff 7.8
Searched_HMMs 46136
Date Fri Aug 16 21:08:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15121hhsearch_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 6.8E-36 1.5E-40 314.1 11.1 194 264-485 12-209 (210)
2 cd01645 RT_Rtv RT_Rtv: Reverse 100.0 9.9E-34 2.1E-38 297.7 12.6 193 264-486 12-213 (213)
3 cd03715 RT_ZFREV_like RT_ZFREV 100.0 9.7E-32 2.1E-36 282.5 12.0 154 604-760 45-210 (210)
4 cd01645 RT_Rtv RT_Rtv: Reverse 100.0 8.2E-29 1.8E-33 260.5 11.3 149 604-760 45-213 (213)
5 cd01644 RT_pepA17 RT_pepA17: R 100.0 1.1E-28 2.3E-33 257.7 10.0 144 312-460 15-175 (213)
6 cd01647 RT_LTR RT_LTR: Reverse 99.9 9.5E-27 2E-31 236.6 11.1 151 309-466 17-167 (177)
7 cd01647 RT_LTR RT_LTR: Reverse 99.9 1E-25 2.2E-30 229.0 11.3 154 604-760 18-177 (177)
8 cd01644 RT_pepA17 RT_pepA17: R 99.9 9.1E-26 2E-30 235.6 8.3 161 594-761 3-188 (213)
9 cd03714 RT_DIRS1 RT_DIRS1: Rev 99.9 4.4E-24 9.5E-29 203.6 6.9 118 355-486 1-119 (119)
10 cd03714 RT_DIRS1 RT_DIRS1: Rev 99.9 5.1E-22 1.1E-26 189.4 8.6 110 649-760 1-119 (119)
11 PF00078 RVT_1: Reverse transc 99.5 5.2E-14 1.1E-18 147.9 8.6 152 309-465 1-201 (214)
12 PF00078 RVT_1: Reverse transc 99.4 6.7E-13 1.4E-17 139.4 9.5 156 604-760 2-214 (214)
13 cd00304 RT_like RT_like: Rever 99.2 8.3E-11 1.8E-15 107.9 8.0 92 649-760 1-98 (98)
14 cd00304 RT_like RT_like: Rever 99.1 1.8E-10 3.8E-15 105.7 5.9 82 355-464 1-84 (98)
15 cd06222 RnaseH RNase H (RNase 98.8 1.6E-08 3.5E-13 96.0 9.3 116 64-181 1-128 (130)
16 cd06222 RnaseH RNase H (RNase 98.7 3.7E-08 8E-13 93.5 8.4 116 810-927 1-128 (130)
17 cd03487 RT_Bac_retron_II RT_Ba 98.6 1.3E-07 2.7E-12 99.9 10.8 127 637-764 50-199 (214)
18 cd01648 TERT TERT: Telomerase 98.6 9.1E-08 2E-12 91.1 7.5 102 649-761 1-119 (119)
19 PRK07708 hypothetical protein; 98.5 5.2E-07 1.1E-11 94.6 9.6 140 789-928 53-205 (219)
20 PRK13907 rnhA ribonuclease H; 98.4 9.5E-07 2.1E-11 85.3 9.6 116 809-927 2-123 (128)
21 PF00075 RNase_H: RNase H; In 98.4 4.3E-07 9.3E-12 87.9 6.0 110 807-926 2-128 (132)
22 PF00075 RNase_H: RNase H; In 98.4 5.2E-07 1.1E-11 87.3 6.3 111 62-180 3-128 (132)
23 COG0328 RnhA Ribonuclease HI [ 98.3 7.3E-07 1.6E-11 87.1 5.6 119 807-928 2-142 (154)
24 cd01648 TERT TERT: Telomerase 98.3 6.5E-07 1.4E-11 85.2 4.9 110 355-486 1-118 (119)
25 PRK13907 rnhA ribonuclease H; 98.3 2.9E-06 6.2E-11 82.0 8.7 116 63-181 2-123 (128)
26 cd01651 RT_G2_intron RT_G2_int 98.3 1.5E-06 3.2E-11 92.3 7.1 120 640-760 66-226 (226)
27 cd01650 RT_nLTR_like RT_nLTR: 98.3 1.5E-06 3.3E-11 91.9 7.0 99 641-748 79-188 (220)
28 cd03487 RT_Bac_retron_II RT_Ba 98.2 1.3E-06 2.9E-11 92.2 6.2 170 311-494 1-203 (214)
29 PRK00203 rnhA ribonuclease H; 98.2 4E-06 8.6E-11 83.3 9.1 115 808-927 3-138 (150)
30 cd01646 RT_Bac_retron_I RT_Bac 98.2 2.5E-06 5.4E-11 85.6 5.8 90 672-762 49-146 (158)
31 PRK07708 hypothetical protein; 98.1 1.1E-05 2.3E-10 84.8 9.5 162 21-182 31-205 (219)
32 PRK06548 ribonuclease H; Provi 98.1 1.8E-05 3.8E-10 78.9 10.1 115 807-928 4-139 (161)
33 PRK07238 bifunctional RNase H/ 98.0 2.2E-05 4.9E-10 90.1 9.5 119 808-928 2-129 (372)
34 PRK00203 rnhA ribonuclease H; 97.9 5.7E-05 1.2E-09 75.0 9.4 114 63-181 4-138 (150)
35 cd01650 RT_nLTR_like RT_nLTR: 97.9 1.8E-05 3.9E-10 83.7 5.8 100 347-464 79-187 (220)
36 PRK08719 ribonuclease H; Revie 97.8 5.7E-05 1.2E-09 74.5 8.0 113 807-927 3-143 (147)
37 PRK07238 bifunctional RNase H/ 97.8 7.2E-05 1.6E-09 85.9 9.1 119 62-182 2-129 (372)
38 PF13456 RVT_3: Reverse transc 97.7 4.6E-05 9.9E-10 67.7 5.6 81 97-180 2-82 (87)
39 PF13456 RVT_3: Reverse transc 97.7 4.1E-05 8.9E-10 68.1 4.3 81 843-926 2-82 (87)
40 COG0328 RnhA Ribonuclease HI [ 97.6 0.00027 5.8E-09 69.4 9.2 119 62-182 3-142 (154)
41 PRK06548 ribonuclease H; Provi 97.6 0.00045 9.7E-09 68.9 10.4 113 62-181 5-138 (161)
42 PRK08719 ribonuclease H; Revie 97.5 0.00041 8.8E-09 68.5 8.6 113 62-181 4-143 (147)
43 cd01651 RT_G2_intron RT_G2_int 97.4 0.00024 5.2E-09 75.3 6.3 114 346-464 66-211 (226)
44 PF00336 DNA_pol_viral_C: DNA 97.4 0.0003 6.5E-09 70.1 6.1 99 64-182 96-194 (245)
45 PF00336 DNA_pol_viral_C: DNA 97.4 0.00037 8E-09 69.5 6.6 102 807-928 93-194 (245)
46 cd01646 RT_Bac_retron_I RT_Bac 97.2 0.00068 1.5E-08 68.0 7.0 94 384-487 50-145 (158)
47 PF05380 Peptidase_A17: Pao re 97.1 0.0014 3E-08 65.8 7.4 79 781-860 45-144 (159)
48 KOG3752|consensus 96.7 0.0055 1.2E-07 67.6 8.6 119 807-928 211-362 (371)
49 KOG3752|consensus 95.5 0.066 1.4E-06 59.3 9.8 119 63-182 213-362 (371)
50 cd01709 RT_like_1 RT_like_1: A 93.8 0.21 4.5E-06 55.5 8.2 70 675-746 82-155 (346)
51 PF07727 RVT_2: Reverse transc 91.9 0.045 9.7E-07 59.0 -0.1 87 349-435 76-183 (246)
52 PF05380 Peptidase_A17: Pao re 90.8 0.42 9.2E-06 47.9 5.6 75 36-111 46-141 (159)
53 KOG4768|consensus 86.4 1.9 4.1E-05 50.7 7.5 129 634-763 350-563 (796)
54 cd01709 RT_like_1 RT_like_1: A 84.3 2.3 4.9E-05 47.5 6.7 98 356-464 56-156 (346)
55 PF07727 RVT_2: Reverse transc 83.6 0.36 7.9E-06 52.0 0.2 111 643-767 76-216 (246)
56 cd01699 RNA_dep_RNAP RNA_dep_R 54.1 30 0.00065 37.7 6.8 61 702-763 194-257 (278)
57 KOG4768|consensus 33.8 26 0.00057 41.7 2.2 121 339-464 349-546 (796)
58 KOG1005|consensus 26.3 92 0.002 38.9 5.1 77 672-749 630-714 (888)
59 PF05869 Dam: DNA N-6-adenine- 23.0 77 0.0017 32.5 3.2 33 183-215 10-42 (181)
60 PF05919 Mitovir_RNA_pol: Mito 20.8 3.3E+02 0.0071 32.3 7.9 135 606-747 94-277 (498)
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=6.8e-36 Score=314.05 Aligned_cols=194 Identities=15% Similarity=0.194 Sum_probs=174.0
Q ss_pred hhHhHHHHHhhcCCCCCCCCCCCCeeeccCCCCCcccCCCCCCcccccCCC-cEEEEEeChhhhhcccCCCCCCCCcchH
Q psy15121 264 VAEGLLVSRLEGAGNSPPNNGSRPQIASDRSSNGLLSGNDRGHDIGNLANT-GLSIMFNLKSLNSYVTTKKFKLINHQKI 342 (960)
Q Consensus 264 ~~~~~~~~~~~~~~~~~~~~~s~p~~~~~~~~~~~~~~~~~~~~i~~kk~g-~~R~~~D~r~lN~~~~~~~~plp~i~~~ 342 (960)
..++.++++|+++.+.|.|+++. +.+.++.+. |+||+| ++|+|+|||.||+.|..+.+++|+++++
T Consensus 12 ~~~~~~~~~v~~ll~~G~I~~~~---------s~~~sp~~~----V~Kk~g~~~R~~vD~r~lN~~~~~~~~~~p~~~~~ 78 (210)
T cd03715 12 EAREGITPHIQELLEAGILVPCQ---------SPWNTPILP----VKKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTL 78 (210)
T ss_pred HHHHHHHHHHHHHHHCCCeECCC---------CCCCCceEE----EEeCCCCcceEEEEhhhhhhcccccCcCCCcHHHH
Confidence 34455889999999999998763 234567777 999999 9999999999999999999999999999
Q ss_pred hhhhc-CCcEEEEeeccccccccccCccccceEEEEEcCeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHH--cCCeeeE
Q psy15121 343 PLFLQ-KNDYLATIDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRE--RGVRCLV 419 (960)
Q Consensus 343 l~~l~-~~~~~s~lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~--~~~~~~~ 419 (960)
+.++. ++++|+++|+++|||||+|+|+++++|||++++|.|+|++||||++|||++||+.|+.++..+.. .+..+.+
T Consensus 79 l~~l~~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~y~~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~ 158 (210)
T cd03715 79 LSLLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQ 158 (210)
T ss_pred HHHhccCCeEEEEeeccCeEEEEEcccccEEeEEEEECCeeEEEEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEE
Confidence 99996 89999999999999999999999999999999999999999999999999999999999988753 3456889
Q ss_pred EecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCccccccCeEEecCChHHHHHHHHhh
Q psy15121 420 YLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLVANHTVVLQSDNKTVITYIRKQ 485 (960)
Q Consensus 420 YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~~~~~v~~~~~~~~~i~~lg~~ 485 (960)
|+|||+|++++.+||.+++.++ +.+|+++|+.++++||.+.. .+ ++|||+.
T Consensus 159 Y~DDili~s~~~~e~~~~l~~v-----~~~l~~~gl~l~~~K~~~~~-----~~-----v~fLG~~ 209 (210)
T cd03715 159 YVDDLLLAADSEEDCLKGTDAL-----LTHLGELGYKVSPKKAQICR-----AE-----VKFLGVV 209 (210)
T ss_pred ECCcEEEecCCHHHHHHHHHHH-----HHHHHHCCCCcCHHHeeCCC-----Cc-----eEEeeEE
Confidence 9999999999999999999999 99999999999999999854 22 6677764
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=9.9e-34 Score=297.74 Aligned_cols=193 Identities=16% Similarity=0.147 Sum_probs=164.4
Q ss_pred hhHhHHHHHhhcCCCCCCCCCCCCeeeccCCCCCcccCCCCCCcccccCCCcEEEEEeChhhhhcccCCCCCCCCcchHh
Q psy15121 264 VAEGLLVSRLEGAGNSPPNNGSRPQIASDRSSNGLLSGNDRGHDIGNLANTGLSIMFNLKSLNSYVTTKKFKLINHQKIP 343 (960)
Q Consensus 264 ~~~~~~~~~~~~~~~~~~~~~s~p~~~~~~~~~~~~~~~~~~~~i~~kk~g~~R~~~D~r~lN~~~~~~~~plp~i~~~l 343 (960)
...+.+.++|+++.+.+.|++|. +.+.|+.+. |+||+|++|+|+|||.||+.+.++.+..+.+. +.
T Consensus 12 ~~~~~~~~~i~~ll~~g~I~~~~---------s~~~sp~~~----v~K~~g~~R~~~D~r~lN~~~~~~~~~~~~~p-~~ 77 (213)
T cd01645 12 EKLEALTELVTEQLKEGHIEPST---------SPWNTPVFV----IKKKSGKWRLLHDLRAVNAQTQDMGALQPGLP-HP 77 (213)
T ss_pred HHHHHHHHHHHHHHHCCceecCC---------CCCcCcEEE----EEcCCCCeEEEechHHHhhhcccccccCCCCC-Ch
Confidence 34445899999999999999874 224567777 99999999999999999999988754222221 12
Q ss_pred hhhcCCcEEEEeeccccccccccCccccceEEEEEc-------CeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHc--C
Q psy15121 344 LFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFLYK-------GTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRER--G 414 (960)
Q Consensus 344 ~~l~~~~~~s~lDl~~~y~qi~l~~~d~~~taf~~~-------~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~~--~ 414 (960)
+.+.++++|+++|+++|||||+++|+++.+|||+|+ +|.|+|++||||+++||++||++|+.++..+... +
T Consensus 78 ~~l~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~~~~~~~~~~~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~ 157 (213)
T cd01645 78 AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGPAKRYQWKVLPQGMKNSPTICQSFVAQALEPFRKQYPD 157 (213)
T ss_pred HHcCCCceEEEEEccCcEEEeeeccCCcceeEEEeccccCCCCCceEEEEEeCCCCcChHHHHHHHHHHHHHHHHHHCCC
Confidence 467899999999999999999999999999999995 7999999999999999999999999999988543 3
Q ss_pred CeeeEEecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCccccccCeEEecCChHHHHHHHHhhc
Q psy15121 415 VRCLVYLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLVANHTVVLQSDNKTVITYIRKQV 486 (960)
Q Consensus 415 ~~~~~YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~~~~~v~~~~~~~~~i~~lg~~v 486 (960)
..+.+|+|||+|++++.++|.+++..+ +++|+++|+.+|++||.+. .+ ++|||+.|
T Consensus 158 ~~~~~Y~DDili~s~~~~~~~~~l~~v-----~~~l~~~gl~ln~~K~~~~------~~-----v~fLG~~i 213 (213)
T cd01645 158 IVIYHYMDDILIASDLEGQLREIYEEL-----RQTLLRWGLTIPPEKVQKE------PP-----FQYLGYEL 213 (213)
T ss_pred eEEEEEcCCEEEEcCCHHHHHHHHHHH-----HHHHHHCCCEeCHHHEeCC------CC-----eEeccEeC
Confidence 357899999999999999999999999 8899999999999998762 23 78888754
No 3
>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=99.97 E-value=9.7e-32 Score=282.55 Aligned_cols=154 Identities=27% Similarity=0.360 Sum_probs=145.0
Q ss_pred ccCCC-CeeEEeecccccccccCCCCcCCChhhHhhhcC-CCcEEEeeehhhccCcccccccccccceee-----eeecc
Q psy15121 604 LYGDG-TMRPVFNLKSLNSYVTTKKFKLINHQKIPLFLQ-KNDYLATIDLSQAYCHIPIARRHRRFLCFL-----IPMDM 676 (960)
Q Consensus 604 ~kk~g-k~R~~vD~r~LN~~~~~~~~plp~i~~~l~~l~-~~~~fs~lDl~~ay~qI~l~~~d~~~taF~-----y~~~r 676 (960)
+||+| ++|+|+|||.||+.+..+.+++|++++++..+. ++++|+++|+++|||||+|+++++++|||+ |+|++
T Consensus 45 ~Kk~g~~~R~~vD~r~lN~~~~~~~~~~p~~~~~l~~l~~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~y~~~~ 124 (210)
T cd03715 45 KKPGGNDYRMVQDLRLVNQAVLPIHPAVPNPYTLLSLLPPKHQWYTVLDLANAFFSLPLAPDSQPLFAFEWEGQQYTFTR 124 (210)
T ss_pred EeCCCCcceEEEEhhhhhhcccccCcCCCcHHHHHHHhccCCeEEEEeeccCeEEEEEcccccEEeEEEEECCeeEEEEE
Confidence 58899 999999999999999999999999999999986 899999999999999999999999999999 99999
Q ss_pred cccCCCCccccchhhHHHhhHhhhc-----CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCccccccc
Q psy15121 677 SSFRPSLSSPGVCPTIKLGRRLRER-----GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIPSH 751 (960)
Q Consensus 677 lPFG~l~~ap~~f~~~~i~~~l~~~-----~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~~~~ 751 (960)
|||| +++||++|+ +.|..+|... +..+.+|+|||+|++++.++|.++++.|+++|+++|+.+|++||+++.+
T Consensus 125 lp~G-l~~sp~~f~-~~~~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~e~~~~l~~v~~~l~~~gl~l~~~K~~~~~~- 201 (210)
T cd03715 125 LPQG-FKNSPTLFH-EALARDLAPFPLEHEGTILLQYVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSPKKAQICRA- 201 (210)
T ss_pred Eecc-ccCcHHHHH-HHHHHHHHHHHhhCCCeEEEEECCcEEEecCCHHHHHHHHHHHHHHHHHCCCCcCHHHeeCCCC-
Confidence 9999 999999998 6777666654 5578999999999999999999999999999999999999999999885
Q ss_pred eEEEEEEEE
Q psy15121 752 RVDYLGISW 760 (960)
Q Consensus 752 ~~~fLG~~i 760 (960)
+++|||++|
T Consensus 202 ~v~fLG~~~ 210 (210)
T cd03715 202 EVKFLGVVW 210 (210)
T ss_pred ceEEeeEEC
Confidence 999999985
No 4
>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=99.95 E-value=8.2e-29 Score=260.46 Aligned_cols=149 Identities=22% Similarity=0.258 Sum_probs=132.5
Q ss_pred ccCCCCeeEEeecccccccccCCCC---cCCChhhHhhhcCCCcEEEeeehhhccCcccccccccccceee---------
Q psy15121 604 LYGDGTMRPVFNLKSLNSYVTTKKF---KLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFL--------- 671 (960)
Q Consensus 604 ~kk~gk~R~~vD~r~LN~~~~~~~~---plp~i~~~l~~l~~~~~fs~lDl~~ay~qI~l~~~d~~~taF~--------- 671 (960)
+||+|++|+|+|||.||+.+.++.+ ++|.. ..+.++++|+++|+++|||||+++++++++|||.
T Consensus 45 ~K~~g~~R~~~D~r~lN~~~~~~~~~~~~~p~~----~~l~~~~~~s~lDl~~af~~i~l~~~~~~~taf~~~~~~~~~~ 120 (213)
T cd01645 45 KKKSGKWRLLHDLRAVNAQTQDMGALQPGLPHP----AALPKGWPLIVLDLKDCFFSIPLHPDDRERFAFTVPSINNKGP 120 (213)
T ss_pred EcCCCCeEEEechHHHhhhcccccccCCCCCCh----HHcCCCceEEEEEccCcEEEeeeccCCcceeEEEeccccCCCC
Confidence 5889999999999999999988754 34433 3568899999999999999999999999999994
Q ss_pred ---eeecccccCCCCccccchhhHHHhhHhhhc-----CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeeccc
Q psy15121 672 ---IPMDMSSFRPSLSSPGVCPTIKLGRRLRER-----GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLK 743 (960)
Q Consensus 672 ---y~~~rlPFG~l~~ap~~f~~~~i~~~l~~~-----~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~ 743 (960)
|+|++|||| +++||++|+ +.|..++..+ +..+.+|+|||+|++++.++|.++++.++++|+++|+.+|++
T Consensus 121 ~~~~~~~~lP~G-l~~SP~~f~-~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~~~~~~~l~~v~~~l~~~gl~ln~~ 198 (213)
T cd01645 121 AKRYQWKVLPQG-MKNSPTICQ-SFVAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPPE 198 (213)
T ss_pred CceEEEEEeCCC-CcChHHHHH-HHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCHHHHHHHHHHHHHHHHHCCCEeCHH
Confidence 999999999 999999998 5777776554 336889999999999999999999999999999999999999
Q ss_pred CccccccceEEEEEEEE
Q psy15121 744 KSQIIPSHRVDYLGISW 760 (960)
Q Consensus 744 K~~~~~~~~~~fLG~~i 760 (960)
||++. .+++||||.|
T Consensus 199 K~~~~--~~v~fLG~~i 213 (213)
T cd01645 199 KVQKE--PPFQYLGYEL 213 (213)
T ss_pred HEeCC--CCeEeccEeC
Confidence 99984 3999999975
No 5
>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=99.95 E-value=1.1e-28 Score=257.65 Aligned_cols=144 Identities=19% Similarity=0.223 Sum_probs=132.6
Q ss_pred CCCcEEEEEeCh------hhhhcccCCCCCCCCcchHhhhhcCCcEEEEeeccccccccccCccccceEEEEEcC-----
Q psy15121 312 ANTGLSIMFNLK------SLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFLYKG----- 380 (960)
Q Consensus 312 k~g~~R~~~D~r------~lN~~~~~~~~plp~i~~~l~~l~~~~~~s~lDl~~~y~qi~l~~~d~~~taf~~~~----- 380 (960)
++||+|+|+||| +||+.+..+++++|++.+++.+++++++|+++|+++|||||+|+|+|+++|+|.|.+
T Consensus 15 ~~~k~R~V~D~s~~~~g~sLN~~l~~gp~~~~~l~~iL~~~R~~~~~~~~Di~~af~qI~i~~~d~~~~~F~w~~~~~~~ 94 (213)
T cd01644 15 TTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDVLRFLWRKDGDEP 94 (213)
T ss_pred CCCccEEEEecccccCCchhhHHhccCCccccchhhhheeeecCceeEehhHHHhhhheecCcccCceEEEEEeCCCCCC
Confidence 379999999999 699999999999999999999999999999999999999999999999999999965
Q ss_pred --eeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHc----CCeeeEEecceEEEeCCHHHHHHHHHHhhccccccccccCC
Q psy15121 381 --TVYQRTCLSFGLASAPQAFAQLSNWVAVLLRER----GVRCLVYLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSG 454 (960)
Q Consensus 381 --~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~~----~~~~~~YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g 454 (960)
+.|+|+|||||+++||++||++|++++..+... .+.+.+|||||+|+++|.+||...+.++ ++.|++.|
T Consensus 95 ~~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e~~~~~~~v-----~~~L~~~G 169 (213)
T cd01644 95 KPIEYRMTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKRL-----IALLKKGG 169 (213)
T ss_pred cceEEEEEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCCHHHHHHHHHHH-----HHHHHhCC
Confidence 899999999999999999999999999888532 1235699999999999999999999999 88888999
Q ss_pred ceecCC
Q psy15121 455 RRSHPT 460 (960)
Q Consensus 455 ~~~~~~ 460 (960)
|.+...
T Consensus 170 f~l~kw 175 (213)
T cd01644 170 FNLRKW 175 (213)
T ss_pred ccchhc
Confidence 988443
No 6
>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=99.94 E-value=9.5e-27 Score=236.56 Aligned_cols=151 Identities=23% Similarity=0.301 Sum_probs=144.8
Q ss_pred cccCCCcEEEEEeChhhhhcccCCCCCCCCcchHhhhhcCCcEEEEeeccccccccccCccccceEEEEEcCeeEEEEEe
Q psy15121 309 GNLANTGLSIMFNLKSLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCL 388 (960)
Q Consensus 309 ~~kk~g~~R~~~D~r~lN~~~~~~~~plp~i~~~l~~l~~~~~~s~lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~~l 388 (960)
|+|++|++|+|+|+|.||+.+..+.+++|.+++++..+++..+++++|+++||+||+++++++.+++|.++++.|+|++|
T Consensus 17 v~k~~~k~R~~~D~r~ln~~~~~~~~~~p~i~~~~~~~~~~~~~~~~D~~~~~~~i~l~~~~~~~~~~~~~~~~~~~~~~ 96 (177)
T cd01647 17 VKKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRM 96 (177)
T ss_pred EECCCCCEEEEEcCHHHhcccCCCCCCCCCHHHHHHHhhcCcEEEecccccCcceeeeccCChhhceeecCCCccEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHcCCeeeEEecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCcccccc
Q psy15121 389 SFGLASAPQAFAQLSNWVAVLLRERGVRCLVYLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLVAN 466 (960)
Q Consensus 389 PfGl~~aP~~fq~~~~~il~~~~~~~~~~~~YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~~~ 466 (960)
|||+++||.+|++.|+.++..+ .+..+..|+||++|.+.+.++|.+++..+ ...+++.|+.++++||.+..
T Consensus 97 p~G~~~s~~~~~~~~~~~l~~~--~~~~~~~y~DDi~i~~~~~~~~~~~~~~~-----~~~l~~~~~~~~~~K~~~~~ 167 (177)
T cd01647 97 PFGLKNAPATFQRLMNKILGDL--LGDFVEVYLDDILVYSKTEEEHLEHLREV-----LERLREAGLKLNPEKCEFGV 167 (177)
T ss_pred cCCCccHHHHHHHHHHhhhccc--cccccEEEecCccccCCCHHHHHHHHHHH-----HHHHHHcCCEeCHHHceecc
Confidence 9999999999999999999777 56668899999999999999999999999 88888999999999998744
No 7
>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=99.93 E-value=1e-25 Score=229.03 Aligned_cols=154 Identities=22% Similarity=0.299 Sum_probs=145.7
Q ss_pred ccCCCCeeEEeecccccccccCCCCcCCChhhHhhhcCCCcEEEeeehhhccCcccccccccccceee-----eeecccc
Q psy15121 604 LYGDGTMRPVFNLKSLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRFLCFL-----IPMDMSS 678 (960)
Q Consensus 604 ~kk~gk~R~~vD~r~LN~~~~~~~~plp~i~~~l~~l~~~~~fs~lDl~~ay~qI~l~~~d~~~taF~-----y~~~rlP 678 (960)
+|++|++|+|+|+|.+|+.+.++.+++|.+++++..+.+..+++++|+++||+|++++++++++++|. |+|++||
T Consensus 18 ~k~~~k~R~~~D~r~ln~~~~~~~~~~p~i~~~~~~~~~~~~~~~~D~~~~~~~i~l~~~~~~~~~~~~~~~~~~~~~~p 97 (177)
T cd01647 18 KKKDGKLRLCVDYRKLNKVTIKDRYPLPTIDELLEELAGAKVFSKLDLRSGYHQIPLAEESRPKTAFRTPFGLYEYTRMP 97 (177)
T ss_pred ECCCCCEEEEEcCHHHhcccCCCCCCCCCHHHHHHHhhcCcEEEecccccCcceeeeccCChhhceeecCCCccEEEEec
Confidence 58899999999999999999999999999999999999999999999999999999999999999998 9999999
Q ss_pred cCCCCccccchhhHHHhhHhhhc-CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCccccccceEEEEE
Q psy15121 679 FRPSLSSPGVCPTIKLGRRLRER-GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIPSHRVDYLG 757 (960)
Q Consensus 679 FG~l~~ap~~f~~~~i~~~l~~~-~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~~~~~~~fLG 757 (960)
|| +++||..|+ +.+...+... +..+..|+||++|.+.+.++|..+++.++++++++|+.+|++||++.. ++++|||
T Consensus 98 ~G-~~~s~~~~~-~~~~~~l~~~~~~~~~~y~DDi~i~~~~~~~~~~~~~~~~~~l~~~~~~~~~~K~~~~~-~~~~~lG 174 (177)
T cd01647 98 FG-LKNAPATFQ-RLMNKILGDLLGDFVEVYLDDILVYSKTEEEHLEHLREVLERLREAGLKLNPEKCEFGV-PEVEFLG 174 (177)
T ss_pred CC-CccHHHHHH-HHHHhhhccccccccEEEecCccccCCCHHHHHHHHHHHHHHHHHcCCEeCHHHceecc-CceEeee
Confidence 99 999999998 6777777665 667899999999999999999999999999999999999999999988 4999999
Q ss_pred EEE
Q psy15121 758 ISW 760 (960)
Q Consensus 758 ~~i 760 (960)
|++
T Consensus 175 ~~i 177 (177)
T cd01647 175 HIV 177 (177)
T ss_pred EEC
Confidence 974
No 8
>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=99.92 E-value=9.1e-26 Score=235.60 Aligned_cols=161 Identities=18% Similarity=0.212 Sum_probs=142.3
Q ss_pred eeeeccCCCcccCCCCeeEEeecc------cccccccCCCCcCCChhhHhhhcCCCcEEEeeehhhccCccccccccccc
Q psy15121 594 VLHHLNDAQGLYGDGTMRPVFNLK------SLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRF 667 (960)
Q Consensus 594 ~~~~~~~~~~~kk~gk~R~~vD~r------~LN~~~~~~~~plp~i~~~l~~l~~~~~fs~lDl~~ay~qI~l~~~d~~~ 667 (960)
+++|....+..|+.||+|+|+||| +||+.+.++++++|.+.+++.+++++++|+++|+++|||||+|+++|+++
T Consensus 3 y~ph~~V~~~~~~~~k~R~V~D~s~~~~g~sLN~~l~~gp~~~~~l~~iL~~~R~~~~~~~~Di~~af~qI~i~~~d~~~ 82 (213)
T cd01644 3 YLPHHAVIKPSKTTTKLRVVFDASARYNGVSLNDMLLKGPDLLNSLFGVLLRFRQGKIAVSADIEKMFHQVKVRPEDRDV 82 (213)
T ss_pred ccCCceecCCCCCCCccEEEEecccccCCchhhHHhccCCccccchhhhheeeecCceeEehhHHHhhhheecCcccCce
Confidence 456766666667799999999998 69999999999999999999999999999999999999999999999999
Q ss_pred ceee------------eeecccccCCCCccccchhhHHHhhHhhhcCC-------eEEEEecceEEecCCHHHHHHHHHH
Q psy15121 668 LCFL------------IPMDMSSFRPSLSSPGVCPTIKLGRRLRERGV-------RCLVYLDDFLLASQDPIVLKNQILQ 728 (960)
Q Consensus 668 taF~------------y~~~rlPFG~l~~ap~~f~~~~i~~~l~~~~~-------~v~~YvDDili~s~s~eeh~~~l~~ 728 (960)
++|. |+|++|||| +++||++|| +.|...+.+... .+..|||||++++++.+||...+++
T Consensus 83 ~~F~w~~~~~~~~~~~Y~~~~~pFG-~~~AP~~~~-~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~e~~~~~~~ 160 (213)
T cd01644 83 LRFLWRKDGDEPKPIEYRMTVVPFG-AASAPFLAN-RALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLNEAVNVAKR 160 (213)
T ss_pred EEEEEeCCCCCCcceEEEEEEEccC-CccchHHHH-HHHHHHHhhcchhhHHHHHHHeeecccceecCCCHHHHHHHHHH
Confidence 9993 999999999 999999998 688888877642 3579999999999999999999999
Q ss_pred HHHHHHHcCCeecccCccccccceEEEEEEEEc
Q psy15121 729 TLQLLTYLGWQVNLKKSQIIPSHRVDYLGISWD 761 (960)
Q Consensus 729 vl~~l~~~Gl~l~~~K~~~~~~~~~~fLG~~i~ 761 (960)
|+++|++.||.+ ++|.. .+.++||.+..
T Consensus 161 v~~~L~~~Gf~l----~kw~s-n~~~~l~~~~~ 188 (213)
T cd01644 161 LIALLKKGGFNL----RKWAS-NSQEVLDDLPE 188 (213)
T ss_pred HHHHHHhCCccc----hhccc-Cchhhhhcccc
Confidence 999999999977 45544 36677776654
No 9
>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=99.89 E-value=4.4e-24 Score=203.60 Aligned_cols=118 Identities=31% Similarity=0.493 Sum_probs=98.9
Q ss_pred eeccccccccccCccccceEEEEEcCeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHcCCeeeEEecceEEEeCCHHHH
Q psy15121 355 IDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRERGVRCLVYLDDFLLASQDSVVL 434 (960)
Q Consensus 355 lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~~~~~~~~YlDDili~s~s~~e~ 434 (960)
+|+++|||||||+|+|+++|||.++++.|+|+|||||+++||++||++|+.++..++..+..+.+|+|||+|+++|.+.+
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 69999999999999999999999999999999999999999999999999999988766777999999999999984444
Q ss_pred HHHHHHhhcccccc-ccccCCceecCCccccccCeEEecCChHHHHHHHHhhc
Q psy15121 435 KNQIFQTLPVNLSG-NCSRSGRRSHPTHSLVANHTVVLQSDNKTVITYIRKQV 486 (960)
Q Consensus 435 ~~~l~~~~~~~~~~-~l~~~g~~~~~~K~~~~~~~v~~~~~~~~~i~~lg~~v 486 (960)
.+.+... .. +++++|+++|++||.+.. ..+ ++|||+.+
T Consensus 81 ~~~~~~l-----~~~~l~~~gl~ln~~K~~~~~----~~~-----v~fLG~~~ 119 (119)
T cd03714 81 EAVLRHL-----RATLLANLGFTLNLEKSKLGP----TQR-----ITFLGLEL 119 (119)
T ss_pred HHHHHHH-----HHHHHHHcCCccChhhcEecC----CCc-----EEECcEeC
Confidence 4333333 11 578999999999998521 233 77888753
No 10
>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=99.86 E-value=5.1e-22 Score=189.38 Aligned_cols=110 Identities=33% Similarity=0.529 Sum_probs=94.0
Q ss_pred eehhhccCcccccccccccceee-----eeecccccCCCCccccchhhHHHhhHhhh---cCCeEEEEecceEEecCCHH
Q psy15121 649 IDLSQAYCHIPIARRHRRFLCFL-----IPMDMSSFRPSLSSPGVCPTIKLGRRLRE---RGVRCLVYLDDFLLASQDPI 720 (960)
Q Consensus 649 lDl~~ay~qI~l~~~d~~~taF~-----y~~~rlPFG~l~~ap~~f~~~~i~~~l~~---~~~~v~~YvDDili~s~s~e 720 (960)
+|+++|||||||+++++++|||+ |+|++|||| +++||++|| +.|..++.. .+..+.+|+|||+|++++.+
T Consensus 1 lD~~~ay~~i~l~~~~~~~~af~~~~~~~~~~~mp~G-l~~sp~~f~-~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~~ 78 (119)
T cd03714 1 VDLKDAYFHIPILPRSRDLLGFAWQGETYQFKALPFG-LSLAPRVFT-KVVEALLAPLRLLGVRIFSYLDDLLIIASSIK 78 (119)
T ss_pred CchhhceEEEecCCCCcceeeEEECCCcEEEEecCCc-ccchHHHHH-HHHHHHHHHhhcCCeEEEEEecCeEEEeCcHH
Confidence 69999999999999999999999 999999999 999999998 677776654 35689999999999999855
Q ss_pred HHHHHHHHHHH-HHHHcCCeecccCccccccceEEEEEEEE
Q psy15121 721 VLKNQILQTLQ-LLTYLGWQVNLKKSQIIPSHRVDYLGISW 760 (960)
Q Consensus 721 eh~~~l~~vl~-~l~~~Gl~l~~~K~~~~~~~~~~fLG~~i 760 (960)
++...++.+.+ +++++|+++|++||++.++++++|||+++
T Consensus 79 ~~~~~~~~l~~~~l~~~gl~ln~~K~~~~~~~~v~fLG~~~ 119 (119)
T cd03714 79 TSEAVLRHLRATLLANLGFTLNLEKSKLGPTQRITFLGLEL 119 (119)
T ss_pred HHHHHHHHHHHHHHHHcCCccChhhcEecCCCcEEECcEeC
Confidence 55544444444 69999999999999965446999999975
No 11
>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=99.49 E-value=5.2e-14 Score=147.86 Aligned_cols=152 Identities=17% Similarity=0.181 Sum_probs=126.7
Q ss_pred cccCC-CcEEEE----EeChhhhhcccC---------CCCCCCCcch--------HhhhhcCCcEEEEeecccccccccc
Q psy15121 309 GNLAN-TGLSIM----FNLKSLNSYVTT---------KKFKLINHQK--------IPLFLQKNDYLATIDLSQAYCHIPI 366 (960)
Q Consensus 309 ~~kk~-g~~R~~----~D~r~lN~~~~~---------~~~plp~i~~--------~l~~l~~~~~~s~lDl~~~y~qi~l 366 (960)
+||++ |++|++ +++|-+|+++.. .......... .+...++..++.++|++++|++|+.
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 58999 999998 899987777655 1111222221 2557788899999999999999999
Q ss_pred CccccceEEEEEc------------------------CeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHH---cCCeeeE
Q psy15121 367 ARRHRRFLCFLYK------------------------GTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRE---RGVRCLV 419 (960)
Q Consensus 367 ~~~d~~~taf~~~------------------------~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~---~~~~~~~ 419 (960)
++-.+..+.+.++ ...+....+|+|...||.+|+.+|+.+...+.. .+..+..
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 9999999999998 457889999999999999999999999988876 4677999
Q ss_pred EecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCccccc
Q psy15121 420 YLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLVA 465 (960)
Q Consensus 420 YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~~ 465 (960)
|+||+++++++.+++.+.+..+ .+.+++.|+++|++|+...
T Consensus 161 Y~DD~~i~~~~~~~~~~~~~~i-----~~~~~~~gl~ln~~Kt~~~ 201 (214)
T PF00078_consen 161 YADDILIISKSKEELQKILEKI-----SQWLEELGLKLNPEKTKIL 201 (214)
T ss_dssp ETTEEEEEESSHHHHHHHHHHH-----HHHHHHTTSBCSSTTTSCS
T ss_pred eccccEEEECCHHHHHHHHHHH-----HHHHHHCCCEEChHHEEEE
Confidence 9999999999999988888888 7778899999999998873
No 12
>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=99.40 E-value=6.7e-13 Score=139.45 Aligned_cols=156 Identities=25% Similarity=0.329 Sum_probs=121.1
Q ss_pred ccCC-CCeeEE----eecccccccccC------------CCCcCCChh-----hHhhhcCCCcEEEeeehhhccCccccc
Q psy15121 604 LYGD-GTMRPV----FNLKSLNSYVTT------------KKFKLINHQ-----KIPLFLQKNDYLATIDLSQAYCHIPIA 661 (960)
Q Consensus 604 ~kk~-gk~R~~----vD~r~LN~~~~~------------~~~plp~i~-----~~l~~l~~~~~fs~lDl~~ay~qI~l~ 661 (960)
+|++ |++|++ +++|-+|+.+.. ..+..+... +.+....+..++.++|+++||++|+.+
T Consensus 2 pK~~~~~~RpI~~~~~~~r~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Di~~~f~sI~~~ 81 (214)
T PF00078_consen 2 PKKNVGKYRPISIPSVDDRIVQRVLNKRLQPILEPIFSPSQFGFRPGRSCHDIKKLNRFKGYLYFLKLDISKAFDSIPHH 81 (214)
T ss_dssp ESSSSSSEEEE----EBTHHHHHHBHH---------HHHTTSSCSHGCCCHHHHHHHC-CGSSEEEEEECCCCGGGSBBH
T ss_pred CCcCCCCeeEcCCCCcHHHHHHHHHHhhccccccccCCCCCCCCcccccccccccccccccccccceeccccccccceee
Confidence 4778 999998 788877766544 122222221 225577888999999999999999999
Q ss_pred ccccccceee-----------------------------eeecccccCCCCccccchh--hHHHhhHhhh---cCCeEEE
Q psy15121 662 RRHRRFLCFL-----------------------------IPMDMSSFRPSLSSPGVCP--TIKLGRRLRE---RGVRCLV 707 (960)
Q Consensus 662 ~~d~~~taF~-----------------------------y~~~rlPFG~l~~ap~~f~--~~~i~~~l~~---~~~~v~~ 707 (960)
+-.+.+..+. +....+|+| ...||.+|. +..+...+.. .+..+..
T Consensus 82 ~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~glpqG-~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~r 160 (214)
T PF00078_consen 82 RLLRKLKRFGVPKKLIRLIQNLLSDRTAKVYLDGDLSPYFQKRGLPQG-SPLSPLLFNIYLDDLDRELQQELNPDISYLR 160 (214)
T ss_dssp TTTGGGGEEEEECCSCHHHHHHHHHHHH-EECGCSSSEEEEESBS-TT-STCHHHHHHHHHHHHHHHHHHHS-TTSEEEE
T ss_pred eccccccccccccccccccccccccccccccccccccccccccccccc-ccccchhhccccccccccccccccccccceE
Confidence 8888666544 456789999 999999983 2334444444 3568999
Q ss_pred EecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCcccc-ccceEEEEEEEE
Q psy15121 708 YLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQII-PSHRVDYLGISW 760 (960)
Q Consensus 708 YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~-~~~~~~fLG~~i 760 (960)
|+||+++.+.+.+++...++.+.+.++++|+.+|++|+... .+.+++|||+.|
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 99999999999999999999999999999999999999987 235999999986
No 13
>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=99.15 E-value=8.3e-11 Score=107.86 Aligned_cols=92 Identities=21% Similarity=0.314 Sum_probs=78.1
Q ss_pred eehhhccCcccccccccccceeeeeecccccCCCCccccchh--hHHHhhHhhh--cCCeEEEEecceEEecCCHHHHHH
Q psy15121 649 IDLSQAYCHIPIARRHRRFLCFLIPMDMSSFRPSLSSPGVCP--TIKLGRRLRE--RGVRCLVYLDDFLLASQDPIVLKN 724 (960)
Q Consensus 649 lDl~~ay~qI~l~~~d~~~taF~y~~~rlPFG~l~~ap~~f~--~~~i~~~l~~--~~~~v~~YvDDili~s~s~eeh~~ 724 (960)
+|++++|+||+ +||| ...||.+|+ +..+...+.. .+..+..|+||+++.+++. ++..
T Consensus 1 ~d~~~~~~~~~-----------------lPqG-~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~-~~~~ 61 (98)
T cd00304 1 FDVKSFFTSIP-----------------LPQG-SPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE-QQAV 61 (98)
T ss_pred CCHHHcCCCCc-----------------cCCC-CchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-HHHH
Confidence 59999999999 9999 999999995 2333333332 2568999999999999999 8999
Q ss_pred HHHHHHHHHHHcCCeecccCccc--cccceEEEEEEEE
Q psy15121 725 QILQTLQLLTYLGWQVNLKKSQI--IPSHRVDYLGISW 760 (960)
Q Consensus 725 ~l~~vl~~l~~~Gl~l~~~K~~~--~~~~~~~fLG~~i 760 (960)
.+..+.+.++++|+.+|++||++ .. +.++|||+++
T Consensus 62 ~~~~l~~~l~~~gl~ln~~Kt~~~~~~-~~~~flG~~~ 98 (98)
T cd00304 62 KKRELEEFLARLGLNLSDEKTQFTEKE-KKFKFLGILV 98 (98)
T ss_pred HHHHHHHHHHHcCcEEChheeEEecCC-CCeeeeceeC
Confidence 99999999999999999999997 55 5999999974
No 14
>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=99.06 E-value=1.8e-10 Score=105.69 Aligned_cols=82 Identities=13% Similarity=0.186 Sum_probs=72.4
Q ss_pred eeccccccccccCccccceEEEEEcCeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHH--cCCeeeEEecceEEEeCCHH
Q psy15121 355 IDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRE--RGVRCLVYLDDFLLASQDSV 432 (960)
Q Consensus 355 lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~--~~~~~~~YlDDili~s~s~~ 432 (960)
+|++++|+||+ ||||...||.+|+.+|+.+...+.+ .+..+..|+||+++++++.
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 59999999999 9999999999999999999988754 4566889999999999998
Q ss_pred HHHHHHHHhhccccccccccCCceecCCcccc
Q psy15121 433 VLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLV 464 (960)
Q Consensus 433 e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~ 464 (960)
++...+..+ .+.+++.|+.+|++|+..
T Consensus 58 ~~~~~~~~l-----~~~l~~~gl~ln~~Kt~~ 84 (98)
T cd00304 58 QQAVKKREL-----EEFLARLGLNLSDEKTQF 84 (98)
T ss_pred HHHHHHHHH-----HHHHHHcCcEEChheeEE
Confidence 777777777 667788999999999877
No 15
>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=98.81 E-value=1.6e-08 Score=96.00 Aligned_cols=116 Identities=20% Similarity=0.186 Sum_probs=88.8
Q ss_pred EEEEcCCcc------cceeeecccccccccChhh--hccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHh
Q psy15121 64 FMSTDASDV------GWGAMVGNVSVQGVWTQAQ--RSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 135 (960)
Q Consensus 64 ~v~tDAS~~------G~ga~l~~~~~~~~~~~~e--~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~ 135 (960)
.++||||.. |+|+++.+......|.... ...+++..|++|++.|++... .....++.|++||..++..+++
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 378999966 9999998654444443333 367899999999999998865 5677889999999999999997
Q ss_pred hCCCCChhhHHHHHHHHHHHHhcCceEEEEeeCC----CchhhhhhhccC
Q psy15121 136 QGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPG----KCNSLADALSRQ 181 (960)
Q Consensus 136 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hipg----~~N~~ADalSR~ 181 (960)
........+..+...+..+. .....+++.|+|| ..|..||+|+|.
T Consensus 80 ~~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~ 128 (130)
T cd06222 80 WYEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKE 128 (130)
T ss_pred cccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHh
Confidence 54334455666666665554 3455688899999 999999999874
No 16
>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=98.71 E-value=3.7e-08 Score=93.50 Aligned_cols=116 Identities=19% Similarity=0.191 Sum_probs=84.9
Q ss_pred EEEeCCCcc------ceeeeEeeeeecccccccc--ccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHHh
Q psy15121 810 FMSTDASDV------GWGAMVGNVSVQGVWTQAQ--RSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 881 (960)
Q Consensus 810 ~l~tDAS~~------g~GavL~q~~~S~~l~~~e--~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~~ 881 (960)
.++||||-. |+|+++.+......+.... ..+++.+.|+.|++.|++.+. .....++.|+||++.++..+++
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 378999876 9999998752111121111 578999999999999999866 5667899999999999999997
Q ss_pred cCCCCChhHHHHHHHHHHHHhccCcEEEEEeeCC----CCCCccccccCC
Q psy15121 882 QGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPG----KCNSLADALSRQ 927 (960)
Q Consensus 882 ~~~~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG----~~N~~AD~LSR~ 927 (960)
........+......+..++.+ ...+.+.|||+ ..|..||.|+|.
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 5433344555666666666622 23445569999 999999999984
No 17
>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=98.65 E-value=1.3e-07 Score=99.95 Aligned_cols=127 Identities=19% Similarity=0.238 Sum_probs=93.1
Q ss_pred hhhcCCCcEEEeeehhhccCcccccccccccc---------eee-----eeecccccCCCCccccch--hhHHHhhHhh-
Q psy15121 637 PLFLQKNDYLATIDLSQAYCHIPIARRHRRFL---------CFL-----IPMDMSSFRPSLSSPGVC--PTIKLGRRLR- 699 (960)
Q Consensus 637 l~~l~~~~~fs~lDl~~ay~qI~l~~~d~~~t---------aF~-----y~~~rlPFG~l~~ap~~f--~~~~i~~~l~- 699 (960)
.....+..++.++|++++|.+|.-+.=-+.+. ... ..-..+|+| ...||.++ .+..+...+.
T Consensus 50 ~~~~~~~~~v~~~Di~~fFdsI~~~~L~~~l~~~~~~~~~~~~~l~~~~~~~~GlpQG-~~lSp~Lanl~l~~~d~~l~~ 128 (214)
T cd03487 50 AKPHCGAKYVLKLDIKDFFPSITFERVRGVFRSLGYFSPDVATILAKLCTYNGHLPQG-APTSPALSNLVFRKLDERLSK 128 (214)
T ss_pred HHHhcCCCEEEEeehhhhcccCCHHHHHHHHHHcCCCCHHHHHHHHHHHhCCCCcCCC-CcccHHHHHHHHHHHHHHHHH
Confidence 33456789999999999999997543111000 000 112389999 99999988 2334444332
Q ss_pred ---hcCCeEEEEecceEEecCCHH--HHHHHHHHHHHHHHHcCCeecccCcccccc-ceEEEEEEEEcCCC
Q psy15121 700 ---ERGVRCLVYLDDFLLASQDPI--VLKNQILQTLQLLTYLGWQVNLKKSQIIPS-HRVDYLGISWDTDL 764 (960)
Q Consensus 700 ---~~~~~v~~YvDDili~s~s~e--eh~~~l~~vl~~l~~~Gl~l~~~K~~~~~~-~~~~fLG~~i~~~g 764 (960)
..+.....|+||+++.+++.+ +....+..+.+.|.+.|+.+|++|+..... ....|||+.++.+.
T Consensus 129 ~~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~i~~~~~~~~~~G~~i~~~~ 199 (214)
T cd03487 129 LAKSNGLTYTRYADDITFSSNKKLKEALDKLLEIIRSILSEEGFKINKSKTRISSKGSRQIVTGLVVNNGK 199 (214)
T ss_pred HHHHcCCeEEEEeccEEEEccccchhHHHHHHHHHHHHHHHCCceeCCCceEEccCCCCcEEEEEEEeCCc
Confidence 346788999999999999987 677788888888899999999999986542 37899999999873
No 18
>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=98.60 E-value=9.1e-08 Score=91.10 Aligned_cols=102 Identities=22% Similarity=0.193 Sum_probs=79.4
Q ss_pred eehhhccCcccccccccccceeeee-ecccccCCCCccccchh--hHHHhhHhhh------cCCeEEEEecceEEecCCH
Q psy15121 649 IDLSQAYCHIPIARRHRRFLCFLIP-MDMSSFRPSLSSPGVCP--TIKLGRRLRE------RGVRCLVYLDDFLLASQDP 719 (960)
Q Consensus 649 lDl~~ay~qI~l~~~d~~~taF~y~-~~rlPFG~l~~ap~~f~--~~~i~~~l~~------~~~~v~~YvDDili~s~s~ 719 (960)
.|++++|-+|+. .|. -+-+|+| ...||.+|. +..+...+.. .+.....|+||+++.+.+.
T Consensus 1 ~d~~~~~~~~~~----------~~~~~~GlpQG-~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~ 69 (119)
T cd01648 1 TDIKKCYDSIPQ----------YYRQKVGIPQG-SPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSL 69 (119)
T ss_pred CChHHhccchhh----------hhhhcCcccCC-cchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCH
Confidence 389999999988 233 3459999 999999982 2333333322 1446788999999999999
Q ss_pred HHHHHHHHHHHHHH-HHcCCeecccCcccc-------ccceEEEEEEEEc
Q psy15121 720 IVLKNQILQTLQLL-TYLGWQVNLKKSQII-------PSHRVDYLGISWD 761 (960)
Q Consensus 720 eeh~~~l~~vl~~l-~~~Gl~l~~~K~~~~-------~~~~~~fLG~~i~ 761 (960)
++....+..+.+.+ ++.|+.+|++|++.. ..+.+.|||+.++
T Consensus 70 ~~~~~~~~~l~~~l~~~~gl~iN~~Kt~~~~~~~~~~~~~~~~flG~~i~ 119 (119)
T cd01648 70 DKAIKFLNLLLRGFINQYKTFVNFDKTQINFSFAQLDSSDLIPWCGLLIN 119 (119)
T ss_pred HHHHHHHHHHHHhhHHhhCeEECcccceeeccccccCCCCccCceeEeeC
Confidence 98888888888888 999999999999864 3457899999875
No 19
>PRK07708 hypothetical protein; Validated
Probab=98.48 E-value=5.2e-07 Score=94.61 Aligned_cols=140 Identities=16% Similarity=0.115 Sum_probs=99.6
Q ss_pred hhhhhhhhcCCCCCCCCC-CceEEEeCCCc------cceeeeEeeeeeccc--c---ccccccCChhHHHHHHHHHHHHh
Q psy15121 789 LKWFYHNLTGFTPLHPPV-PRTFMSTDASD------VGWGAMVGNVSVQGV--W---TQAQRSWHINLKELFTVRAAISS 856 (960)
Q Consensus 789 l~w~~~~l~~f~~l~~p~-~~~~l~tDAS~------~g~GavL~q~~~S~~--l---~~~e~~ysi~~kEllAiv~Al~~ 856 (960)
..|+.+.++-......+. ..+++|+|||- .|+|+|+........ + ..-....+.++.|..|++.|++.
T Consensus 53 ~~~~~k~~~~~~~~~~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~ 132 (219)
T PRK07708 53 TEWSLKELKKLSKEVEEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQE 132 (219)
T ss_pred CEeeHHHHhhhhhhhccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHH
Confidence 446555555444432222 35899999965 688888864211000 1 11112358889999999999997
Q ss_pred Ccccc-CCCeEEEEcCCHHHHHHHHhcCCCCChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCCccccccCCC
Q psy15121 857 NPSLV-ANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQA 928 (960)
Q Consensus 857 ~~~~L-~g~~~~I~TDh~~l~~~l~~~~~~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~~AD~LSR~~ 928 (960)
....- ...+++|++|++.++.++++.-..+++.+..+..+....+.+|.+.+.++|||.+.|..||.|++..
T Consensus 133 A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~A 205 (219)
T PRK07708 133 LEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQA 205 (219)
T ss_pred HHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHH
Confidence 65432 2235899999999999999765567777778888888888899877777899999999999999854
No 20
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.43 E-value=9.5e-07 Score=85.30 Aligned_cols=116 Identities=16% Similarity=0.198 Sum_probs=83.6
Q ss_pred eEEEeCCCc------cceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHHhc
Q psy15121 809 TFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQ 882 (960)
Q Consensus 809 ~~l~tDAS~------~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~~~ 882 (960)
+.||||||- .|+|+|+........++......+.++.|+.|++.||+.... +...++.|+||++.++..+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEechHHHHHHHhHH
Confidence 468999854 688999854311111222234468899999999999997543 2235799999999999999974
Q ss_pred CCCCChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCCccccccCC
Q psy15121 883 GGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQ 927 (960)
Q Consensus 883 ~~~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~~AD~LSR~ 927 (960)
. .+...+...+.....++.+|... .+.|+|+..|..||.|+|.
T Consensus 81 ~-~~~~~~~~l~~~~~~l~~~f~~~-~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 81 Y-AKNKMFAPLLEEALQYIKSFDLF-FIKWIPSSQNKVADELARK 123 (128)
T ss_pred H-hcChhHHHHHHHHHHHHhcCCce-EEEEcCchhchhHHHHHHH
Confidence 3 23345566677777778888754 3479999999999999984
No 21
>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=98.39 E-value=4.3e-07 Score=87.95 Aligned_cols=110 Identities=18% Similarity=0.186 Sum_probs=72.6
Q ss_pred CceEEEeCCCc------cceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHH
Q psy15121 807 PRTFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIR 880 (960)
Q Consensus 807 ~~~~l~tDAS~------~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~ 880 (960)
..+++|||||- .|+|.++... +.++..-...++++.|+.|+..||+.+ ...+++|+||++.++..++
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 4777755322 223222227799999999999999954 2289999999999999777
Q ss_pred h-----cCC-CCChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCC-----ccccccC
Q psy15121 881 K-----QGG-LRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNS-----LADALSR 926 (960)
Q Consensus 881 ~-----~~~-~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~-----~AD~LSR 926 (960)
. ... ..... ....++...+ .....+.+.||||+.|. .||.|+|
T Consensus 75 ~~~~~~~~~~~~~~~--~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk 128 (132)
T PF00075_consen 75 KWLHGNGWKKTSNGR--PIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAK 128 (132)
T ss_dssp THHHHTTSBSCTSSS--BHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred Hhccccccccccccc--cchhheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHH
Confidence 6 211 11110 1223444444 33666777899999765 5888876
No 22
>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=98.37 E-value=5.2e-07 Score=87.34 Aligned_cols=111 Identities=20% Similarity=0.207 Sum_probs=76.0
Q ss_pred ceEEEEcCCc------ccceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHh
Q psy15121 62 RTFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 135 (960)
Q Consensus 62 ~~~v~tDAS~------~G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~ 135 (960)
..++|||||- .|+|.+..... .++..-...+++.-||+|+..||+.+ ....+.|+||++.++..+++
T Consensus 3 ~~~iytDgS~~~~~~~~~~g~v~~~~~---~~~~~~~~~s~~~aEl~Ai~~AL~~~----~~~~v~I~tDS~~v~~~l~~ 75 (132)
T PF00075_consen 3 AIIIYTDGSCRPNPGKGGAGYVVWGGR---NFSFRLGGQSNNRAELQAIIEALKAL----EHRKVTIYTDSQYVLNALNK 75 (132)
T ss_dssp SEEEEEEEEECTTTTEEEEEEEEETTE---EEEEEEESECHHHHHHHHHHHHHHTH----STSEEEEEES-HHHHHHHHT
T ss_pred cEEEEEeCCccCCCCceEEEEEEECCe---EEEecccccchhhhheehHHHHHHHh----hcccccccccHHHHHHHHHH
Confidence 3579999993 37777664331 33322227789999999999999965 22889999999999998876
Q ss_pred h----CCCCChhhHHHHHHHHHHHHhcCceEEEEeeCCC-----chhhhhhhcc
Q psy15121 136 Q----GGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGK-----CNSLADALSR 180 (960)
Q Consensus 136 ~----~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hipg~-----~N~~ADalSR 180 (960)
. +-........+..+++..+ ..+..+.+.|+||. .|..||.|.|
T Consensus 76 ~~~~~~~~~~~~~~~i~~~i~~~~-~~~~~v~~~~V~~H~~~~~~N~~aD~lAk 128 (132)
T PF00075_consen 76 WLHGNGWKKTSNGRPIKNEIWELL-SRGIKVRFRWVPGHSGVPQGNERADRLAK 128 (132)
T ss_dssp HHHHTTSBSCTSSSBHTHHHHHHH-HHSSEEEEEESSSSSSSHHHHHHHHHHHH
T ss_pred hccccccccccccccchhheeecc-ccceEEeeeeccCcCCCchhHHHHHHHHH
Confidence 1 1111111113445666666 44778999999999 4558999876
No 23
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.31 E-value=7.3e-07 Score=87.12 Aligned_cols=119 Identities=20% Similarity=0.198 Sum_probs=84.6
Q ss_pred CceEEEeCCCc------cceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHH
Q psy15121 807 PRTFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIR 880 (960)
Q Consensus 807 ~~~~l~tDAS~------~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~ 880 (960)
....||||++. .|+|+||.-.-..+.++..+..-+.++.|+.|++.||+..+. +....++|+|||+.++..++
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 35689999964 689999983322334566666789999999999999998775 56688999999999997777
Q ss_pred hc----------CCC-CChhHHHHHHHHHHHHhcc-CcEEEEEeeCCCC----CCccccccCCC
Q psy15121 881 KQ----------GGL-RSHALLAETKKLLLIMSKL-NIHIVPYFIPGKC----NSLADALSRQA 928 (960)
Q Consensus 881 ~~----------~~~-~~~~l~~~~~r~~~~l~~~-~~~i~~~~vpG~~----N~~AD~LSR~~ 928 (960)
.- ... +.-....+..+..+.+.++ .+.+ +||+|+. |..||.|.|..
T Consensus 81 ~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~--~WVkgH~g~~~NeraD~LA~~~ 142 (154)
T COG0328 81 RWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFW--EWVKGHAGHPENERADQLAREA 142 (154)
T ss_pred HHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEE--EEeeCCCCChHHHHHHHHHHHH
Confidence 21 000 0111223456667778888 5554 5999765 66799998844
No 24
>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=98.30 E-value=6.5e-07 Score=85.25 Aligned_cols=110 Identities=14% Similarity=0.083 Sum_probs=80.1
Q ss_pred eeccccccccccCccccceEEEEEcCeeEEEE-EeCCCCCCHHHHHHHHHHHHHHHHHHc------CCeeeEEecceEEE
Q psy15121 355 IDLSQAYCHIPIARRHRRFLCFLYKGTVYQRT-CLSFGLASAPQAFAQLSNWVAVLLRER------GVRCLVYLDDFLLA 427 (960)
Q Consensus 355 lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~-~lPfGl~~aP~~fq~~~~~il~~~~~~------~~~~~~YlDDili~ 427 (960)
.|++++|=+|+. .|..+ .+|+|...||.+|.-+|+.+...+.+. +...+.|+||++++
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 388899988888 34433 399999999999999998888776543 34477999999999
Q ss_pred eCCHHHHHHHHHHhhcccccccc-ccCCceecCCccccccCeEEecCChHHHHHHHHhhc
Q psy15121 428 SQDSVVLKNQIFQTLPVNLSGNC-SRSGRRSHPTHSLVANHTVVLQSDNKTVITYIRKQV 486 (960)
Q Consensus 428 s~s~~e~~~~l~~~~~~~~~~~l-~~~g~~~~~~K~~~~~~~v~~~~~~~~~i~~lg~~v 486 (960)
+++.++..+.+..+ ...+ ++.|+.+|++|+....... .......+.|+|..+
T Consensus 66 ~~~~~~~~~~~~~l-----~~~l~~~~gl~iN~~Kt~~~~~~~--~~~~~~~~~flG~~i 118 (119)
T cd01648 66 TTSLDKAIKFLNLL-----LRGFINQYKTFVNFDKTQINFSFA--QLDSSDLIPWCGLLI 118 (119)
T ss_pred eCCHHHHHHHHHHH-----HHhhHHhhCeEECcccceeecccc--ccCCCCccCceeEee
Confidence 99988777666666 4444 7889999999987632100 011223477887754
No 25
>PRK13907 rnhA ribonuclease H; Provisional
Probab=98.27 E-value=2.9e-06 Score=81.96 Aligned_cols=116 Identities=16% Similarity=0.201 Sum_probs=82.6
Q ss_pred eEEEEcCCc------ccceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHhh
Q psy15121 63 TFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQ 136 (960)
Q Consensus 63 ~~v~tDAS~------~G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~~ 136 (960)
.+||||||. .|+|+++.........+......+=+.=|++|++.||+.-.. +.-+++.|++|++-++..+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~-~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTE-HNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHh-CCCCEEEEEechHHHHHHHhHH
Confidence 368999884 478999853221111111112235578899999999977532 2235799999999999999974
Q ss_pred CCCCChhhHHHHHHHHHHHHhcCceEEEEeeCCCchhhhhhhccC
Q psy15121 137 GGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQ 181 (960)
Q Consensus 137 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hipg~~N~~ADalSR~ 181 (960)
. .+.+.+..+...+..+..++.. +...|+|+..|..||+|.|.
T Consensus 81 ~-~~~~~~~~l~~~~~~l~~~f~~-~~~~~v~r~~N~~Ad~LA~~ 123 (128)
T PRK13907 81 Y-AKNKMFAPLLEEALQYIKSFDL-FFIKWIPSSQNKVADELARK 123 (128)
T ss_pred H-hcChhHHHHHHHHHHHHhcCCc-eEEEEcCchhchhHHHHHHH
Confidence 3 3456788888888777766543 55699999999999999874
No 26
>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=98.26 E-value=1.5e-06 Score=92.31 Aligned_cols=120 Identities=22% Similarity=0.304 Sum_probs=87.4
Q ss_pred cCCCcEEEeeehhhccCccccc-------cc--cccc---------------ceeeeeecccccCCCCccccch--hhHH
Q psy15121 640 LQKNDYLATIDLSQAYCHIPIA-------RR--HRRF---------------LCFLIPMDMSSFRPSLSSPGVC--PTIK 693 (960)
Q Consensus 640 l~~~~~fs~lDl~~ay~qI~l~-------~~--d~~~---------------taF~y~~~rlPFG~l~~ap~~f--~~~~ 693 (960)
..+..++.++|++++|..|.-+ .. +... ......-..+|+| ...||.+| .+..
T Consensus 66 ~~~~~~~~~~Di~~~Fdsi~~~~l~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~GlpqG-~~lSp~L~~~~l~~ 144 (226)
T cd01651 66 KGGYTWVIEGDIKGFFDNIDHDLLLKILKRRIGDKRVLRLIRKWLKAGVLEDGKLVETEKGTPQG-GVISPLLANIYLHE 144 (226)
T ss_pred cCCCeEEEEccHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHHHhceEccCCeEeCCCCCcCCC-ccHHHHHHHHHHHH
Confidence 4567899999999999988521 10 0000 0000334568999 99999877 2233
Q ss_pred HhhHhhh-------------cCCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCccccc--cceEEEEEE
Q psy15121 694 LGRRLRE-------------RGVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIP--SHRVDYLGI 758 (960)
Q Consensus 694 i~~~l~~-------------~~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~~--~~~~~fLG~ 758 (960)
+...+.. .+.....|+||+++.+.+.++....++.+.+.+++.|+.+|++|++... .+.+.|||+
T Consensus 145 ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~~~~~~gl~ln~~Kt~i~~~~~~~~~fLG~ 224 (226)
T cd01651 145 LDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEELGLELNPEKTRITHFKSEGFDFLGF 224 (226)
T ss_pred HHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHHHHHHcCCeechhhcceeecCCCCCeeCCe
Confidence 3333332 3457889999999999999988888888889999999999999998765 368999998
Q ss_pred EE
Q psy15121 759 SW 760 (960)
Q Consensus 759 ~i 760 (960)
.+
T Consensus 225 ~~ 226 (226)
T cd01651 225 TF 226 (226)
T ss_pred EC
Confidence 64
No 27
>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=98.25 E-value=1.5e-06 Score=91.87 Aligned_cols=99 Identities=21% Similarity=0.218 Sum_probs=78.6
Q ss_pred CCCcEEEeeehhhccCcccccccccccceeeeeecccccCCCCccccchh--hHHHhhHhh--------hcCCeEEEEec
Q psy15121 641 QKNDYLATIDLSQAYCHIPIARRHRRFLCFLIPMDMSSFRPSLSSPGVCP--TIKLGRRLR--------ERGVRCLVYLD 710 (960)
Q Consensus 641 ~~~~~fs~lDl~~ay~qI~l~~~d~~~taF~y~~~rlPFG~l~~ap~~f~--~~~i~~~l~--------~~~~~v~~YvD 710 (960)
.+..++.++|+++||..|+-+.-.+.. .+|+| ...||.+|. +..+.+.+. ..+..+..|+|
T Consensus 79 ~~~~~~l~~Di~~aFdsi~~~~l~~~l--------GipQG-~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaD 149 (220)
T cd01650 79 KKSLVLVFLDFEKAFDSVDHEFLLKAL--------GVRQG-DPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYAD 149 (220)
T ss_pred CCceEEEEEEHHhhcCcCCHHHHHHHh--------CCccC-CcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEecc
Confidence 456899999999999988744222211 79999 999999883 344555554 23557899999
Q ss_pred ceEEecCCHH-HHHHHHHHHHHHHHHcCCeecccCcccc
Q psy15121 711 DFLLASQDPI-VLKNQILQTLQLLTYLGWQVNLKKSQII 748 (960)
Q Consensus 711 Dili~s~s~e-eh~~~l~~vl~~l~~~Gl~l~~~K~~~~ 748 (960)
|+++++.+.+ .....++.+...+.+.|+.+|++||++.
T Consensus 150 D~~i~~~~~~~~~~~~~~~~~~~~~~~gl~in~~Kt~~~ 188 (220)
T cd01650 150 DIVLFSEGKSRKLQELLQRLQEWSKESGLKINPSKSKVM 188 (220)
T ss_pred ceeeeccCCHHHHHHHHHHHHHHHHHcCCEEChhheEEE
Confidence 9999999988 8888888888999999999999999875
No 28
>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=98.24 E-value=1.3e-06 Score=92.18 Aligned_cols=170 Identities=15% Similarity=0.141 Sum_probs=108.9
Q ss_pred cCCCcEEEEEeCh--------hhhhcccC-CCC------CCCC--cchHhhhhcCCcEEEEeeccccccccccCccccce
Q psy15121 311 LANTGLSIMFNLK--------SLNSYVTT-KKF------KLIN--HQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRF 373 (960)
Q Consensus 311 kk~g~~R~~~D~r--------~lN~~~~~-~~~------plp~--i~~~l~~l~~~~~~s~lDl~~~y~qi~l~~~d~~~ 373 (960)
|++|+.|.+.--. .||..+.. ..+ -.|. ..+....-.+..++.++|++++|-.|.-+.=-...
T Consensus 1 k~~g~~R~I~~p~~~~r~iq~~l~~~l~~~~~~~~~~~g~~~grs~~~~~~~~~~~~~v~~~Di~~fFdsI~~~~L~~~l 80 (214)
T cd03487 1 KKNGGFRTIYAPKPELKAIQRKILSNLLSKLPVHDAAHGFVKGRSIITNAKPHCGAKYVLKLDIKDFFPSITFERVRGVF 80 (214)
T ss_pred CCCCCeeeEeCCCHHHHHHHHHHHHHHhccCCCCcceeeecCCCCHHHHHHHhcCCCEEEEeehhhhcccCCHHHHHHHH
Confidence 6788999877632 35555531 110 1232 33333444578899999999999998875411111
Q ss_pred EEEEEc-C---------eeEEEEEeCCCCCCHHHHHHHHHHHHHHHHH----HcCCeeeEEecceEEEeCCHH--HHHHH
Q psy15121 374 LCFLYK-G---------TVYQRTCLSFGLASAPQAFAQLSNWVAVLLR----ERGVRCLVYLDDFLLASQDSV--VLKNQ 437 (960)
Q Consensus 374 taf~~~-~---------~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~----~~~~~~~~YlDDili~s~s~~--e~~~~ 437 (960)
...... . -.+ -..+|+|...||.+|.-+|+.+-..+. ..+.....|+||+++++++.+ +..+.
T Consensus 81 ~~~~~~~~~~~~~l~~~~~~-~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~ 159 (214)
T cd03487 81 RSLGYFSPDVATILAKLCTY-NGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLKEALDKL 159 (214)
T ss_pred HHcCCCCHHHHHHHHHHHhC-CCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccchhHHHHH
Confidence 111110 0 001 117999999999999999887765553 457778899999999999876 44444
Q ss_pred HHHhhccccccccccCCceecCCccccccCeEEecCChHHHHHHHHhhccccchhhH
Q psy15121 438 IFQTLPVNLSGNCSRSGRRSHPTHSLVANHTVVLQSDNKTVITYIRKQVGLRSNALL 494 (960)
Q Consensus 438 l~~~~~~~~~~~l~~~g~~~~~~K~~~~~~~v~~~~~~~~~i~~lg~~v~~~~~~~~ 494 (960)
+..+ -..+++.|+.+|++|+.... .++ -+.|+|..+......+.
T Consensus 160 ~~~i-----~~~l~~~gL~ln~~Kt~i~~------~~~--~~~~~G~~i~~~~~~~~ 203 (214)
T cd03487 160 LEII-----RSILSEEGFKINKSKTRISS------KGS--RQIVTGLVVNNGKPSLP 203 (214)
T ss_pred HHHH-----HHHHHHCCceeCCCceEEcc------CCC--CcEEEEEEEeCCcCCCC
Confidence 4444 34466889999999977632 111 26788888876655544
No 29
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.24 E-value=4e-06 Score=83.32 Aligned_cols=115 Identities=19% Similarity=0.205 Sum_probs=73.8
Q ss_pred ceEEEeCCCc------cceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHHh
Q psy15121 808 RTFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 881 (960)
Q Consensus 808 ~~~l~tDAS~------~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~~ 881 (960)
.+.||||+|- .|+|+++...-....++..+...+.++.||.|++.||+... ....+.|+|||+.++..++.
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 3789999985 57778775321111233334456788999999999999764 34679999999988776664
Q ss_pred -------c---CCCCCh-hHHHHHHHHHHHHhccCcEEEEEeeCCCC----CCccccccCC
Q psy15121 882 -------Q---GGLRSH-ALLAETKKLLLIMSKLNIHIVPYFIPGKC----NSLADALSRQ 927 (960)
Q Consensus 882 -------~---~~~~~~-~l~~~~~r~~~~l~~~~~~i~~~~vpG~~----N~~AD~LSR~ 927 (960)
+ .....+ .....+.++..++....+.+ .||||+. |..||.|+|.
T Consensus 80 w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~--~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 80 WIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKW--HWVKGHAGHPENERCDELARA 138 (150)
T ss_pred HHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEE--EEecCCCCCHHHHHHHHHHHH
Confidence 0 000000 11123344555555555554 5999877 7789999873
No 30
>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=98.16 E-value=2.5e-06 Score=85.60 Aligned_cols=90 Identities=21% Similarity=0.331 Sum_probs=74.4
Q ss_pred eeecccccCCCCccccch--hhHHHhhHhhh--cCCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCccc
Q psy15121 672 IPMDMSSFRPSLSSPGVC--PTIKLGRRLRE--RGVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQI 747 (960)
Q Consensus 672 y~~~rlPFG~l~~ap~~f--~~~~i~~~l~~--~~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~ 747 (960)
.....+|+| ...||.++ .+..+...+.. .+.....|+||+++.+++.+.....++.+-+.+.+.|+.+|++|+..
T Consensus 49 ~~~~GlpqG-~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l~~~gL~ln~~Kt~~ 127 (158)
T cd01646 49 GQTNGLPIG-PLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEI 127 (158)
T ss_pred CCCceEccC-cchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHHHHCCCEEChhhcee
Confidence 445689999 99999888 23455555555 36789999999999999999988899999999999999999999987
Q ss_pred cccce----EEEEEEEEcC
Q psy15121 748 IPSHR----VDYLGISWDT 762 (960)
Q Consensus 748 ~~~~~----~~fLG~~i~~ 762 (960)
....+ .+|||+.+..
T Consensus 128 ~~~~~~~~~~~flg~~~~~ 146 (158)
T cd01646 128 LPLPEGTASKDFLGYRFSP 146 (158)
T ss_pred eecCCCCccccccceEeeh
Confidence 66544 6999999975
No 31
>PRK07708 hypothetical protein; Validated
Probab=98.11 E-value=1.1e-05 Score=84.84 Aligned_cols=162 Identities=17% Similarity=0.138 Sum_probs=111.5
Q ss_pred hHHHHHhhhhceEeccHhhhhHHHhHHHHhcCCCCCCCCCCc-eEEEEcCCc------ccceeeeccccccccc--C---
Q psy15121 21 VLKNQILQTLQLLTYLAQALIELKWFYHNLTGFTPLHPPVPR-TFMSTDASD------VGWGAMVGNVSVQGVW--T--- 88 (960)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~dl~ww~~~L~~~~~l~~~~~~-~~v~tDAS~------~G~ga~l~~~~~~~~~--~--- 88 (960)
.+..++-++-+...+.-.=..+..|=..-|--.+.-....|. .++|+|||- .|+|+++........+ .
T Consensus 31 ~~~~~~~~~~~~~~~~~~d~~~~~~~~k~~~~~~~~~~~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~ 110 (219)
T PRK07708 31 QLAEDFEKTGRVKELEFYDEMDTEWSLKELKKLSKEVEEEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNA 110 (219)
T ss_pred HHHHHHhhcCCceeEEEecCCCCEeeHHHHhhhhhhhccCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeec
Confidence 445556666666666555556666766666444444444444 599999985 5788888532111111 1
Q ss_pred hhhhccccchHhHHHHHHHHHhCCCc-cCCCeEEEEecChhHHHHHHhhCCCCChhhHHHHHHHHHHHHhcCceEEEEee
Q psy15121 89 QAQRSWHINLKELFTVRAAISSNPSL-VANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFI 167 (960)
Q Consensus 89 ~~e~~~~i~~~Ellav~~Al~~~~~~-~~~~~v~~~~Dn~~av~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hi 167 (960)
.-....+-|.-|+.|++.||+.-... ....+|.|++|++-++.++++.-..+++.+..+...+...+.++.+.++..||
T Consensus 111 ~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~V 190 (219)
T PRK07708 111 YIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPI 190 (219)
T ss_pred cccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEEC
Confidence 11112356777999999999765332 22235999999999999999766677888888888887777777777899999
Q ss_pred CCCchhhhhhhccCC
Q psy15121 168 PGKCNSLADALSRQA 182 (960)
Q Consensus 168 pg~~N~~ADalSR~~ 182 (960)
|.++|-.||.|.+..
T Consensus 191 pR~~N~~AD~LAk~A 205 (219)
T PRK07708 191 SRKQNKEADQLATQA 205 (219)
T ss_pred CchhhhHHHHHHHHH
Confidence 999999999998764
No 32
>PRK06548 ribonuclease H; Provisional
Probab=98.09 E-value=1.8e-05 Score=78.89 Aligned_cols=115 Identities=23% Similarity=0.270 Sum_probs=77.8
Q ss_pred CceEEEeCCCc------cceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHH
Q psy15121 807 PRTFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIR 880 (960)
Q Consensus 807 ~~~~l~tDAS~------~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~ 880 (960)
..++||||+|. .|+|+++... ...+..+..-+.++.||.|++.||+.... .+.+++|+|||+.++..++
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 34899999864 4677776522 22344455668899999999999975442 2357999999999998888
Q ss_pred h--------c--CCCCCh-hHHHHHHHHHHHHhccCcEEEEEeeCCCC----CCccccccCCC
Q psy15121 881 K--------Q--GGLRSH-ALLAETKKLLLIMSKLNIHIVPYFIPGKC----NSLADALSRQA 928 (960)
Q Consensus 881 ~--------~--~~~~~~-~l~~~~~r~~~~l~~~~~~i~~~~vpG~~----N~~AD~LSR~~ 928 (960)
+ . .....+ .....++.+..++.+..+++ .||+|+. |..||.|.|..
T Consensus 79 ~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~--~wVkgHsg~~gNe~aD~LA~~a 139 (161)
T PRK06548 79 KWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRM--SWVNAHTGHPLNEAADSLARQA 139 (161)
T ss_pred HHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEE--EEEecCCCCHHHHHHHHHHHHH
Confidence 4 1 111111 11234455566666666555 5999987 78899999853
No 33
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.97 E-value=2.2e-05 Score=90.10 Aligned_cols=119 Identities=18% Similarity=0.243 Sum_probs=88.2
Q ss_pred ceEEEeCCCc------cceeeeEeeeeec---cccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHH
Q psy15121 808 RTFMSTDASD------VGWGAMVGNVSVQ---GVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAY 878 (960)
Q Consensus 808 ~~~l~tDAS~------~g~GavL~q~~~S---~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~ 878 (960)
.++||||||- .|+|+++...... ..+.......+.++.|+.|++.||+..... ...+++|+||++.++..
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 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAEL-GATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhC-CCCeEEEEeCcHHHHHH
Confidence 4689999964 5888888753111 112223335678899999999999975433 45689999999999999
Q ss_pred HHhcCCCCChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCCccccccCCC
Q psy15121 879 IRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQA 928 (960)
Q Consensus 879 l~~~~~~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~~AD~LSR~~ 928 (960)
+++....++..+...+.+...++.+|. .+++.|||++.|..||.|++..
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~-~~~i~~v~r~~N~~AD~LA~~a 129 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFG-RVTYTWIPRARNAHADRLANEA 129 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCC-ceEEEECCchhhhHHHHHHHHH
Confidence 987544566677677767777778876 3455799999999999999954
No 34
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.88 E-value=5.7e-05 Score=75.04 Aligned_cols=114 Identities=19% Similarity=0.190 Sum_probs=72.7
Q ss_pred eEEEEcCCc------ccceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHh-
Q psy15121 63 TFMSTDASD------VGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK- 135 (960)
Q Consensus 63 ~~v~tDAS~------~G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~- 135 (960)
..||||+|. -|+|+++........++..+....-|.-||+|++.||+.... ++.+.|+||++.++.-+++
T Consensus 4 v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~---~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 4 VEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE---PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred EEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC---CCeEEEEECHHHHHHHHHHH
Confidence 579999995 468888752221112232333445677899999999986542 4679999999877765553
Q ss_pred ---------hCCCCCh-hhHHHHHHHHHHHHhcCceEEEEeeCCCc----hhhhhhhccC
Q psy15121 136 ---------QGGLRSH-ALLAETKKLLLIMSKLNIHIVPYFIPGKC----NSLADALSRQ 181 (960)
Q Consensus 136 ---------~~~~~~~-~~~~l~~~l~~~~~~~~~~~~~~hipg~~----N~~ADalSR~ 181 (960)
..+...+ ...++...+..+... ..+.+.|+||.. |..||.|.|.
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~AD~lA~~ 138 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERCDELARA 138 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHHHHHHHH
Confidence 1011111 123455555544433 457789999665 9999999874
No 35
>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=97.86 E-value=1.8e-05 Score=83.69 Aligned_cols=100 Identities=22% Similarity=0.275 Sum_probs=80.0
Q ss_pred cCCcEEEEeeccccccccccCccccceEEEEEcCeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHH--------cCCeee
Q psy15121 347 QKNDYLATIDLSQAYCHIPIARRHRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRE--------RGVRCL 418 (960)
Q Consensus 347 ~~~~~~s~lDl~~~y~qi~l~~~d~~~taf~~~~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~--------~~~~~~ 418 (960)
.+..++.++|++++|-.|+-+.=.... .+|+|...||.+|.-+|+.+...+.. .+..+.
T Consensus 79 ~~~~~~l~~Di~~aFdsi~~~~l~~~l-------------GipQG~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~ 145 (220)
T cd01650 79 KKSLVLVFLDFEKAFDSVDHEFLLKAL-------------GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHL 145 (220)
T ss_pred CCceEEEEEEHHhhcCcCCHHHHHHHh-------------CCccCCcccHHHHHHHHHHHHHHHHhhccccCCCCccceE
Confidence 456799999999999988754433333 89999999999999999999888752 355588
Q ss_pred EEecceEEEeCCHH-HHHHHHHHhhccccccccccCCceecCCcccc
Q psy15121 419 VYLDDFLLASQDSV-VLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLV 464 (960)
Q Consensus 419 ~YlDDili~s~s~~-e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~ 464 (960)
.|.||+++++.+.+ +....+..+ ...+...|+++|++|+.+
T Consensus 146 ~yaDD~~i~~~~~~~~~~~~~~~~-----~~~~~~~gl~in~~Kt~~ 187 (220)
T cd01650 146 AYADDIVLFSEGKSRKLQELLQRL-----QEWSKESGLKINPSKSKV 187 (220)
T ss_pred EeccceeeeccCCHHHHHHHHHHH-----HHHHHHcCCEEChhheEE
Confidence 99999999999988 555555555 445668899999999876
No 36
>PRK08719 ribonuclease H; Reviewed
Probab=97.81 E-value=5.7e-05 Score=74.53 Aligned_cols=113 Identities=14% Similarity=0.054 Sum_probs=69.9
Q ss_pred CceEEEeCCCc---------cceeeeEeee----eeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCH
Q psy15121 807 PRTFMSTDASD---------VGWGAMVGNV----SVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNK 873 (960)
Q Consensus 807 ~~~~l~tDAS~---------~g~GavL~q~----~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~ 873 (960)
.++++|||+|. .|+|+++... ....... .+...+.++.|+.|++.||+.... ..+|+|||+
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 46899999876 2788887532 1111111 122358899999999999998653 247999999
Q ss_pred HHHHHHHh-------c-C--CCCChhH-HHHHHHHHHHHhccCcEEEEEeeCCC----CCCccccccCC
Q psy15121 874 TVIAYIRK-------Q-G--GLRSHAL-LAETKKLLLIMSKLNIHIVPYFIPGK----CNSLADALSRQ 927 (960)
Q Consensus 874 ~l~~~l~~-------~-~--~~~~~~l-~~~~~r~~~~l~~~~~~i~~~~vpG~----~N~~AD~LSR~ 927 (960)
.++..++. + - +...+-. ...+..+..+....++. +.||||+ .|..||.|.|.
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 YCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVE--VEKVTAHSGIEGNEAADMLAQA 143 (147)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEE--EEEecCCCCChhHHHHHHHHHH
Confidence 88877752 1 0 1111111 12233334444544444 5699995 48889998873
No 37
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=97.76 E-value=7.2e-05 Score=85.94 Aligned_cols=119 Identities=18% Similarity=0.231 Sum_probs=87.1
Q ss_pred ceEEEEcCCcc------cceeeecccccc---cccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHH
Q psy15121 62 RTFMSTDASDV------GWGAMVGNVSVQ---GVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAY 132 (960)
Q Consensus 62 ~~~v~tDAS~~------G~ga~l~~~~~~---~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~ 132 (960)
..+||+|||.. |+|+++...... ..++......+-|.=|+.|++.||+.-.. +..+++.|++|++-++.-
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 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAE-LGATEVEVRMDSKLVVEQ 80 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHh-CCCCeEEEEeCcHHHHHH
Confidence 45899999954 789988643211 11222222456678999999999986533 345689999999999988
Q ss_pred HHhhCCCCChhhHHHHHHHHHHHHhcCceEEEEeeCCCchhhhhhhccCC
Q psy15121 133 IRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQA 182 (960)
Q Consensus 133 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hipg~~N~~ADalSR~~ 182 (960)
+++....+++.+..+...+..+...+. .+++.|+|+++|..||+|.+..
T Consensus 81 i~~~~~~~~~~l~~~~~~i~~l~~~f~-~~~i~~v~r~~N~~AD~LA~~a 129 (372)
T PRK07238 81 MSGRWKVKHPDMKPLAAQARELASQFG-RVTYTWIPRARNAHADRLANEA 129 (372)
T ss_pred hCCCCccCChHHHHHHHHHHHHHhcCC-ceEEEECCchhhhHHHHHHHHH
Confidence 886444466778888777777665553 3778999999999999999874
No 38
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.74 E-value=4.6e-05 Score=67.74 Aligned_cols=81 Identities=20% Similarity=0.285 Sum_probs=59.7
Q ss_pred chHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHhhCCCCChhhHHHHHHHHHHHHhcCceEEEEeeCCCchhhhh
Q psy15121 97 NLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLAD 176 (960)
Q Consensus 97 ~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~hipg~~N~~AD 176 (960)
+.-|++|+..||+.-.. +.=++|.|.+|++.++..+++....++ .+..+...+..+...+ -.++..|||...|..||
T Consensus 2 ~~aE~~al~~al~~a~~-~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~-~~~~~~~i~r~~N~~A~ 78 (87)
T PF13456_consen 2 LEAEALALLEALQLAWE-LGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRF-WNVSVSHIPREQNKVAD 78 (87)
T ss_dssp HHHHHHHHHHHHHHHHC-CT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCC-SCEEEEE--GGGSHHHH
T ss_pred cHHHHHHHHHHHHHHHH-CCCCEEEEEecCccccccccccccccc-cccccchhhhhhhccc-cceEEEEEChHHhHHHH
Confidence 35699999999976533 334579999999999999997654555 7788888887766654 33789999999999999
Q ss_pred hhcc
Q psy15121 177 ALSR 180 (960)
Q Consensus 177 alSR 180 (960)
.|+|
T Consensus 79 ~LA~ 82 (87)
T PF13456_consen 79 ALAK 82 (87)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 9987
No 39
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.68 E-value=4.1e-05 Score=68.06 Aligned_cols=81 Identities=20% Similarity=0.278 Sum_probs=60.9
Q ss_pred hHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHHhcCCCCChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCCccc
Q psy15121 843 NLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQGGLRSHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLAD 922 (960)
Q Consensus 843 ~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~~~~~~~~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~~AD 922 (960)
.+.|++|+..|++.... +.-.++++.||++.++..+++...... .+...+..+..++..|+ .+.+.|+|...|..||
T Consensus 2 ~~aE~~al~~al~~a~~-~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~-~~~~~~i~r~~N~~A~ 78 (87)
T PF13456_consen 2 LEAEALALLEALQLAWE-LGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFW-NVSVSHIPREQNKVAD 78 (87)
T ss_dssp HHHHHHHHHHHHHHHHC-CT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCS-CEEEEE--GGGSHHHH
T ss_pred cHHHHHHHHHHHHHHHH-CCCCEEEEEecCccccccccccccccc-cccccchhhhhhhcccc-ceEEEEEChHHhHHHH
Confidence 57899999999998644 344689999999999999997644444 66778888888888865 3445799999999999
Q ss_pred cccC
Q psy15121 923 ALSR 926 (960)
Q Consensus 923 ~LSR 926 (960)
.|+|
T Consensus 79 ~LA~ 82 (87)
T PF13456_consen 79 ALAK 82 (87)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 9987
No 40
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=97.61 E-value=0.00027 Score=69.37 Aligned_cols=119 Identities=19% Similarity=0.175 Sum_probs=80.4
Q ss_pred ceEEEEcCCcc------cceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHh
Q psy15121 62 RTFMSTDASDV------GWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 135 (960)
Q Consensus 62 ~~~v~tDAS~~------G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~ 135 (960)
..+||||+|.. |||+|+.-.......+..+....=|.-|++|++.||+.-.. +.-+.|.|+||++-++.-+++
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~-~~~~~v~l~tDS~yv~~~i~~ 81 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE-LGACEVTLYTDSKYVVEGITR 81 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh-cCCceEEEEecHHHHHHHHHH
Confidence 45899999964 59999872111123455555667788999999999987654 566889999999988876662
Q ss_pred h----------CCCC-ChhhHHHHHHHHHHHHhcCceEEEEeeC----CCchhhhhhhccCC
Q psy15121 136 Q----------GGLR-SHALLAETKKLLLIMSKLNIHIVPYFIP----GKCNSLADALSRQA 182 (960)
Q Consensus 136 ~----------~~~~-~~~~~~l~~~l~~~~~~~~~~~~~~hip----g~~N~~ADalSR~~ 182 (960)
- .+.+ .-...+|-..+......++ .+++.||| ...|..||.|.|..
T Consensus 82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~-~v~~~WVkgH~g~~~NeraD~LA~~~ 142 (154)
T COG0328 82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHE-LVFWEWVKGHAGHPENERADQLAREA 142 (154)
T ss_pred HHhhccccCccccccCccccHHHHHHHHHHHhhCC-eEEEEEeeCCCCChHHHHHHHHHHHH
Confidence 1 0000 0113355555554444432 47889999 67899999998754
No 41
>PRK06548 ribonuclease H; Provisional
Probab=97.58 E-value=0.00045 Score=68.94 Aligned_cols=113 Identities=23% Similarity=0.257 Sum_probs=75.2
Q ss_pred ceEEEEcCCcc------cceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHh
Q psy15121 62 RTFMSTDASDV------GWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRK 135 (960)
Q Consensus 62 ~~~v~tDAS~~------G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~ 135 (960)
..+||||+|.. |||+++... +..+..+..-.=|.-||+|++.||+.... .+..|+|+||++-++.-+++
T Consensus 5 ~~~IytDGa~~gnpg~~G~g~~~~~~---~~~~g~~~~~TNnraEl~Aii~aL~~~~~--~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 5 EIIAATDGSSLANPGPSGWAWYVDEN---TWDSGGWDIATNNIAELTAVRELLIATRH--TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred EEEEEEeeccCCCCCceEEEEEEeCC---cEEccCCCCCCHHHHHHHHHHHHHHhhhc--CCceEEEEeChHHHHHHHHH
Confidence 36899999865 488877522 11222222233466799999999975542 34579999999999988873
Q ss_pred -------hC---CCCCh-hhHHHHHHHHHHHHhcCceEEEEeeCCCc----hhhhhhhccC
Q psy15121 136 -------QG---GLRSH-ALLAETKKLLLIMSKLNIHIVPYFIPGKC----NSLADALSRQ 181 (960)
Q Consensus 136 -------~~---~~~~~-~~~~l~~~l~~~~~~~~~~~~~~hipg~~----N~~ADalSR~ 181 (960)
.+ ++..+ ..++|...|..+....+ +++.|++|.. |..||+|.|.
T Consensus 80 W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~--v~~~wVkgHsg~~gNe~aD~LA~~ 138 (161)
T PRK06548 80 WVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRN--IRMSWVNAHTGHPLNEAADSLARQ 138 (161)
T ss_pred HHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCc--eEEEEEecCCCCHHHHHHHHHHHH
Confidence 11 11222 23666666666555543 6779999866 9999999886
No 42
>PRK08719 ribonuclease H; Reviewed
Probab=97.48 E-value=0.00041 Score=68.50 Aligned_cols=113 Identities=15% Similarity=0.041 Sum_probs=68.8
Q ss_pred ceEEEEcCCc----c-----cceeeeccccccc--ccCh-hhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhH
Q psy15121 62 RTFMSTDASD----V-----GWGAMVGNVSVQG--VWTQ-AQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTV 129 (960)
Q Consensus 62 ~~~v~tDAS~----~-----G~ga~l~~~~~~~--~~~~-~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~a 129 (960)
+.+||||+|. . |+|+++....-.. .++. -+....-|.-||.|++.||+.-... ..|+||++-+
T Consensus 4 ~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~-----~~i~tDS~yv 78 (147)
T PRK08719 4 SYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG-----DVIYSDSDYC 78 (147)
T ss_pred eEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC-----CEEEechHHH
Confidence 4589999986 2 8899875221110 1111 1112356778999999999876432 3799999888
Q ss_pred HHHHHh-------hCCCCChh----hHHHHHHHHHHHHhcCceEEEEeeCC----CchhhhhhhccC
Q psy15121 130 IAYIRK-------QGGLRSHA----LLAETKKLLLIMSKLNIHIVPYFIPG----KCNSLADALSRQ 181 (960)
Q Consensus 130 v~~~~~-------~~~~~~~~----~~~l~~~l~~~~~~~~~~~~~~hipg----~~N~~ADalSR~ 181 (960)
+.-+++ .+-..+.. ..++...|..+.. .-.++..|+|| ..|..||.|.|.
T Consensus 79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~ 143 (147)
T PRK08719 79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQA 143 (147)
T ss_pred HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHH
Confidence 766642 11111111 2333333332222 23388899999 779999998774
No 43
>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=97.40 E-value=0.00024 Score=75.34 Aligned_cols=114 Identities=17% Similarity=0.175 Sum_probs=78.8
Q ss_pred hcCCcEEEEeeccccccccccC-------cc--ccceE--------EEE-EcCe-eEEEEEeCCCCCCHHHHHHHHHHHH
Q psy15121 346 LQKNDYLATIDLSQAYCHIPIA-------RR--HRRFL--------CFL-YKGT-VYQRTCLSFGLASAPQAFAQLSNWV 406 (960)
Q Consensus 346 l~~~~~~s~lDl~~~y~qi~l~-------~~--d~~~t--------af~-~~~~-~y~~~~lPfGl~~aP~~fq~~~~~i 406 (960)
-.+..++.++|++++|-.|+-+ .. +.... ... .... ...-..+|+|...||.+|.-+++.+
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 3556899999999999877421 11 10000 000 0111 1223458999999999999999888
Q ss_pred HHHHHH-------------cCCeeeEEecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCcccc
Q psy15121 407 AVLLRE-------------RGVRCLVYLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLV 464 (960)
Q Consensus 407 l~~~~~-------------~~~~~~~YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~ 464 (960)
...+.. .+...+.|+||+++++++.++..+.+..+ ...++..|+.+|++|+..
T Consensus 146 d~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i-----~~~~~~~gl~ln~~Kt~i 211 (226)
T cd01651 146 DKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELI-----REFLEELGLELNPEKTRI 211 (226)
T ss_pred HHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHH-----HHHHHHcCCeechhhcce
Confidence 776653 34558899999999999988755555555 445668899999999776
No 44
>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=97.38 E-value=0.0003 Score=70.12 Aligned_cols=99 Identities=24% Similarity=0.366 Sum_probs=72.9
Q ss_pred EEEEcCCcccceeeecccccccccChhhhccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHHHHhhCCCCChh
Q psy15121 64 FMSTDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQGGLRSHA 143 (960)
Q Consensus 64 ~v~tDAS~~G~ga~l~~~~~~~~~~~~e~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~~~~~~~~~~~~ 143 (960)
.|++||+-+|||.....+...|.|+. -.+|+.-||+|+-+| ..+.|.+. +.|||+-+. .++.-+-.=.
T Consensus 96 ~VfaDATpTgwgi~i~~~~~~~Tfs~---~l~IhtaELlaaClA-----r~~~~~r~-l~tDnt~Vl---srkyts~PW~ 163 (245)
T PF00336_consen 96 QVFADATPTGWGISITGQRMRGTFSK---PLPIHTAELLAACLA-----RLMSGARC-LGTDNTVVL---SRKYTSFPWL 163 (245)
T ss_pred ceeccCCCCcceeeecCceeeeeecc---cccchHHHHHHHHHH-----HhccCCcE-EeecCcEEE---ecccccCcHH
Confidence 78899999999999988999999987 579999999998776 34456655 889998654 3322121112
Q ss_pred hHHHHHHHHHHHHhcCceEEEEeeCCCchhhhhhhccCC
Q psy15121 144 LLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQA 182 (960)
Q Consensus 144 ~~~l~~~l~~~~~~~~~~~~~~hipg~~N~~ADalSR~~ 182 (960)
+.-+|++| . ++ .+..|+|.+.| =||-=||..
T Consensus 164 lac~A~wi----L-rg--ts~~yVPS~~N-PAD~PsR~~ 194 (245)
T PF00336_consen 164 LACAANWI----L-RG--TSFYYVPSKYN-PADDPSRGK 194 (245)
T ss_pred HHHHHHHh----h-cC--ceEEEeccccC-cCCCCCCCc
Confidence 33344444 3 33 56699999999 799999987
No 45
>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=97.37 E-value=0.00037 Score=69.52 Aligned_cols=102 Identities=25% Similarity=0.345 Sum_probs=69.9
Q ss_pred CceEEEeCCCccceeeeEeeeeeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHHHHHHHHhcCCCC
Q psy15121 807 PRTFMSTDASDVGWGAMVGNVSVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAYIRKQGGLR 886 (960)
Q Consensus 807 ~~~~l~tDAS~~g~GavL~q~~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~l~~~l~~~~~~~ 886 (960)
.-..|++||+.+|||.++......++|+. -.+|+-.||+|..+|.-. .|.++ +.|||..+.+ ++ -..
T Consensus 93 ~lc~VfaDATpTgwgi~i~~~~~~~Tfs~---~l~IhtaELlaaClAr~~-----~~~r~-l~tDnt~Vls---rk-yts 159 (245)
T PF00336_consen 93 GLCQVFADATPTGWGISITGQRMRGTFSK---PLPIHTAELLAACLARLM-----SGARC-LGTDNTVVLS---RK-YTS 159 (245)
T ss_pred CCCceeccCCCCcceeeecCceeeeeecc---cccchHHHHHHHHHHHhc-----cCCcE-EeecCcEEEe---cc-ccc
Confidence 34579999999999999877667777774 468999999999887543 44555 8899997752 11 111
Q ss_pred ChhHHHHHHHHHHHHhccCcEEEEEeeCCCCCCccccccCCC
Q psy15121 887 SHALLAETKKLLLIMSKLNIHIVPYFIPGKCNSLADALSRQA 928 (960)
Q Consensus 887 ~~~l~~~~~r~~~~l~~~~~~i~~~~vpG~~N~~AD~LSR~~ 928 (960)
-+=+-.....|+ . .+..+ .|||++.| +||..||..
T Consensus 160 ~PW~lac~A~wi---L-rgts~--~yVPS~~N-PAD~PsR~~ 194 (245)
T PF00336_consen 160 FPWLLACAANWI---L-RGTSF--YYVPSKYN-PADDPSRGK 194 (245)
T ss_pred CcHHHHHHHHHh---h-cCceE--EEeccccC-cCCCCCCCc
Confidence 111122233333 2 23344 49999999 999999975
No 46
>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=97.23 E-value=0.00068 Score=67.97 Aligned_cols=94 Identities=14% Similarity=0.135 Sum_probs=72.0
Q ss_pred EEEEeCCCCCCHHHHHHHHHHHHHHHHHH--cCCeeeEEecceEEEeCCHHHHHHHHHHhhccccccccccCCceecCCc
Q psy15121 384 QRTCLSFGLASAPQAFAQLSNWVAVLLRE--RGVRCLVYLDDFLLASQDSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTH 461 (960)
Q Consensus 384 ~~~~lPfGl~~aP~~fq~~~~~il~~~~~--~~~~~~~YlDDili~s~s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K 461 (960)
....+|+|...||-+++-+|..+-..+.. .+....-|+||+++++++.++..+.+..+ ...+.+.|+.+|++|
T Consensus 50 ~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i-----~~~l~~~gL~ln~~K 124 (158)
T cd01646 50 QTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEEL-----KEFLAELGLSLNLSK 124 (158)
T ss_pred CCceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHH-----HHHHHHCCCEEChhh
Confidence 45679999999999999999988777765 56668899999999999988766666555 556778999999999
Q ss_pred cccccCeEEecCChHHHHHHHHhhcc
Q psy15121 462 SLVANHTVVLQSDNKTVITYIRKQVG 487 (960)
Q Consensus 462 ~~~~~~~v~~~~~~~~~i~~lg~~v~ 487 (960)
+.... ..... +-..|||+.+.
T Consensus 125 t~~~~----~~~~~-~~~~flg~~~~ 145 (158)
T cd01646 125 TEILP----LPEGT-ASKDFLGYRFS 145 (158)
T ss_pred ceeee----cCCCC-ccccccceEee
Confidence 77633 11211 23678887664
No 47
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=97.08 E-value=0.0014 Score=65.78 Aligned_cols=79 Identities=20% Similarity=0.218 Sum_probs=52.1
Q ss_pred chhhHHHHhhhhhhhhcCCCCCCCCC---------CceEEEeCCCccceeeeEeeee-----------ecc-cccccccc
Q psy15121 781 LQTQALIELKWFYHNLTGFTPLHPPV---------PRTFMSTDASDVGWGAMVGNVS-----------VQG-VWTQAQRS 839 (960)
Q Consensus 781 L~~~l~~~l~w~~~~l~~f~~l~~p~---------~~~~l~tDAS~~g~GavL~q~~-----------~S~-~l~~~e~~ 839 (960)
|..++...+.-|.+.+.....+..|+ .++++|||||..|+|||++-.. .++ +..+ -+.
T Consensus 45 lp~el~~~w~~~~~~l~~~~~i~iPR~i~~~~~~~~~L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P-~k~ 123 (159)
T PF05380_consen 45 LPDELRKEWKKWLKELESLSPIRIPRCIPISDYRSVELHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAP-LKT 123 (159)
T ss_pred hhHHHHHHHHHHHHHHhhcccccCCcccccccccceeeeEeecccccceeeEeEeeeccCCceeeeeeeecccccC-CCC
Confidence 44555555555666555544332221 3689999999999999987542 222 2333 344
Q ss_pred CChhHHHHHHHHHHHHhCccc
Q psy15121 840 WHINLKELFTVRAAISSNPSL 860 (960)
Q Consensus 840 ysi~~kEllAiv~Al~~~~~~ 860 (960)
.+|.++||+|++.|.+.....
T Consensus 124 ~tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 124 VTIPRLELLAALLGVRLANTV 144 (159)
T ss_pred CcHHHHHHHHHHHHHHHHHHH
Confidence 599999999999999865443
No 48
>KOG3752|consensus
Probab=96.70 E-value=0.0055 Score=67.61 Aligned_cols=119 Identities=22% Similarity=0.222 Sum_probs=75.1
Q ss_pred CceEEEeCCCc---------cceeeeEeee---eeccccccccccCChhHHHHHHHHHHHHhCccccCCCeEEEEcCCHH
Q psy15121 807 PRTFMSTDASD---------VGWGAMVGNV---SVQGVWTQAQRSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKT 874 (960)
Q Consensus 807 ~~~~l~tDAS~---------~g~GavL~q~---~~S~~l~~~e~~ysi~~kEllAiv~Al~~~~~~L~g~~~~I~TDh~~ 874 (960)
...+||||+|- .|+|+...-. -.|+.+. -.+-+.+..|+.|+..||++.+.-. ..+++|.||+..
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~--~g~qtNnrAEl~Av~~ALkka~~~~-~~kv~I~TDS~~ 287 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLA--GGRQTNNRAELIAAIEALKKARSKN-INKVVIRTDSEY 287 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCC--CCcccccHHHHHHHHHHHHHHHhcC-CCcEEEEechHH
Confidence 34789999965 3566555432 1222222 1334678999999999999865432 238999999999
Q ss_pred HHHHHHhc---------CCCCCh-------hHHHHHHHHHHHHhc-cCcEEEEEeeCCCC----CCccccccCCC
Q psy15121 875 VIAYIRKQ---------GGLRSH-------ALLAETKKLLLIMSK-LNIHIVPYFIPGKC----NSLADALSRQA 928 (960)
Q Consensus 875 l~~~l~~~---------~~~~~~-------~l~~~~~r~~~~l~~-~~~~i~~~~vpG~~----N~~AD~LSR~~ 928 (960)
++.+++.- +..... ....-.....++.++ -+.++..+||+|+. |..||.|+|..
T Consensus 288 ~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 288 FINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred HHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 99888741 111111 111233444555555 34555667999976 77899999954
No 49
>KOG3752|consensus
Probab=95.54 E-value=0.066 Score=59.34 Aligned_cols=119 Identities=21% Similarity=0.193 Sum_probs=74.0
Q ss_pred eEEEEcCCcc---------cceeeecccccccccChhh-hccccchHhHHHHHHHHHhCCCccCCCeEEEEecChhHHHH
Q psy15121 63 TFMSTDASDV---------GWGAMVGNVSVQGVWTQAQ-RSWHINLKELFTVRAAISSNPSLVANHTVVLQSDNKTVIAY 132 (960)
Q Consensus 63 ~~v~tDAS~~---------G~ga~l~~~~~~~~~~~~e-~~~~i~~~Ellav~~Al~~~~~~~~~~~v~~~~Dn~~av~~ 132 (960)
..||||+|.. |+|+..+.-+..+..-+-. -.-+-|.-||.||..||+.-... ....|+|+||..-++.+
T Consensus 213 ~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-~~~kv~I~TDS~~~i~~ 291 (371)
T KOG3752|consen 213 QVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-NINKVVIRTDSEYFINS 291 (371)
T ss_pred eEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-CCCcEEEEechHHHHHH
Confidence 5899999855 4777776333222111111 22345778999999999875433 23379999999988887
Q ss_pred HHhh---------CCCCChh-------hHHHHHHHHHHHHh-cCceEEEEeeCCCc----hhhhhhhccCC
Q psy15121 133 IRKQ---------GGLRSHA-------LLAETKKLLLIMSK-LNIHIVPYFIPGKC----NSLADALSRQA 182 (960)
Q Consensus 133 ~~~~---------~~~~~~~-------~~~l~~~l~~~~~~-~~~~~~~~hipg~~----N~~ADalSR~~ 182 (960)
++.. .+..+++ .+..-..+-.+... .+..++..|++|.. |.+||+++|.-
T Consensus 292 l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 292 LTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKG 362 (371)
T ss_pred HHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhh
Confidence 7621 0111111 22222333222233 46789999999975 88999999964
No 50
>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=93.75 E-value=0.21 Score=55.55 Aligned_cols=70 Identities=13% Similarity=0.065 Sum_probs=53.4
Q ss_pred cccccCCCCccccch--hhHHHhhHhhhc--CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCcc
Q psy15121 675 DMSSFRPSLSSPGVC--PTIKLGRRLRER--GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQ 746 (960)
Q Consensus 675 ~rlPFG~l~~ap~~f--~~~~i~~~l~~~--~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~ 746 (960)
+-+|+| -.-||-.- .+..+...+... |...+.|.||++++ .+.+++....+.+-++++..|+.+|++|..
T Consensus 82 rGtPqG-gviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~-~~~~~a~~aw~~i~~fl~~lGLelN~eKT~ 155 (346)
T cd01709 82 RGTPMS-HALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFW-GQPETCAKAWKAIQEFAKVMGLELNKEKTG 155 (346)
T ss_pred CccCCC-chhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEE-cCHHHHHHHHHHHHHHHHHcCceeccccce
Confidence 568888 77777543 223444444332 67899999999999 557888888899999999999999999975
No 51
>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=91.90 E-value=0.045 Score=59.00 Aligned_cols=87 Identities=21% Similarity=0.227 Sum_probs=62.8
Q ss_pred CcEEEEeeccccccccccCcccc--ceEEEEEc---CeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHH------------
Q psy15121 349 NDYLATIDLSQAYCHIPIARRHR--RFLCFLYK---GTVYQRTCLSFGLASAPQAFAQLSNWVAVLLR------------ 411 (960)
Q Consensus 349 ~~~~s~lDl~~~y~qi~l~~~d~--~~taf~~~---~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~------------ 411 (960)
+-..-.+|++.||.+=+++++=- .-.+|..+ +..++-..--+||+-||..+...++..|..+.
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 44566789999999999987631 22355554 34466666779999999999988887776552
Q ss_pred -H---cCCeeeEEecceEEEeCCHHHHH
Q psy15121 412 -E---RGVRCLVYLDDFLLASQDSVVLK 435 (960)
Q Consensus 412 -~---~~~~~~~YlDDili~s~s~~e~~ 435 (960)
. ....+.+|+||++|.+.+.++..
T Consensus 156 ~~~~~~~~ii~vYVDDili~~~~~~~i~ 183 (246)
T PF07727_consen 156 KKSGDGFIIILVYVDDILIAGPSEEEIE 183 (246)
T ss_pred ccccccccccccccccccccccccccee
Confidence 1 11336799999999999865433
No 52
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=90.80 E-value=0.42 Score=47.88 Aligned_cols=75 Identities=21% Similarity=0.233 Sum_probs=44.3
Q ss_pred cHhhhhHHHhHHHHhcCCCCCCCC---------CCceEEEEcCCcccceeeecccc-cccc-----------cChhhhcc
Q psy15121 36 LAQALIELKWFYHNLTGFTPLHPP---------VPRTFMSTDASDVGWGAMVGNVS-VQGV-----------WTQAQRSW 94 (960)
Q Consensus 36 ~~~~~~dl~ww~~~L~~~~~l~~~---------~~~~~v~tDAS~~G~ga~l~~~~-~~~~-----------~~~~e~~~ 94 (960)
+.+...+..=|.+.+.....+..| ....|+++|||..|+||+.--+. .++. -.+ -++.
T Consensus 46 p~el~~~w~~~~~~l~~~~~i~iPR~i~~~~~~~~~L~~F~DAS~~aygavvYlr~~~~~~~~~~ll~aKsrv~P-~k~~ 124 (159)
T PF05380_consen 46 PDELRKEWKKWLKELESLSPIRIPRCIPISDYRSVELHVFCDASESAYGAVVYLRSYSDGSVQVRLLFAKSRVAP-LKTV 124 (159)
T ss_pred hHHHHHHHHHHHHHHhhcccccCCcccccccccceeeeEeecccccceeeEeEeeeccCCceeeeeeeecccccC-CCCC
Confidence 344444445566666443322211 12238999999999999874222 1111 111 1334
Q ss_pred ccchHhHHHHHHHHHhC
Q psy15121 95 HINLKELFTVRAAISSN 111 (960)
Q Consensus 95 ~i~~~Ellav~~Al~~~ 111 (960)
+|--+||+|++.|++..
T Consensus 125 tIPRlEL~a~~l~~~l~ 141 (159)
T PF05380_consen 125 TIPRLELLAALLGVRLA 141 (159)
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 89999999999998543
No 53
>KOG4768|consensus
Probab=86.41 E-value=1.9 Score=50.67 Aligned_cols=129 Identities=22% Similarity=0.313 Sum_probs=91.3
Q ss_pred hhHhhhcCCCcEEEeeehhhccCccccccc------ccccceee-------------------eeecccccCCCCccccc
Q psy15121 634 QKIPLFLQKNDYLATIDLSQAYCHIPIARR------HRRFLCFL-------------------IPMDMSSFRPSLSSPGV 688 (960)
Q Consensus 634 ~~~l~~l~~~~~fs~lDl~~ay~qI~l~~~------d~~~taF~-------------------y~~~rlPFG~l~~ap~~ 688 (960)
-++...++|+.||...||++.|-.||-++- -..-..|. +++.-.|+| -..||.+
T Consensus 350 ~~~~n~f~gcnw~ie~DLkkcfdtIphd~LI~eL~~rIkdk~fidL~~kll~AGy~ten~ry~~~~lGtpqg-svvspil 428 (796)
T KOG4768|consen 350 LKTHNLFRGCNWFIEVDLKKCFDTIPHDELIIELQKRIKDKGFIDLNYKLLRAGYTTENARYHVEFLGTPQG-SVVSPIL 428 (796)
T ss_pred HHHHHHhhccceEEechHHHHhccccHHHHHHHHHHHHhhhhHHHHHHHHHhcCccccccceeccccccccc-ccCCchh
Confidence 355667899999999999999999983321 01112232 788888999 8888876
Q ss_pred h--hhHHHhhHhhh-c----------------------------------------------------CC---eEEEEec
Q psy15121 689 C--PTIKLGRRLRE-R----------------------------------------------------GV---RCLVYLD 710 (960)
Q Consensus 689 f--~~~~i~~~l~~-~----------------------------------------------------~~---~v~~YvD 710 (960)
. .++.+.+.|+. . |. .-+.|-|
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 5 12333333332 0 00 1246889
Q ss_pred ceEEec-CCHHHHHHHHHHHHHHHHHcCCeecccCcccccc-ceEEEEEEEEcCC
Q psy15121 711 DFLLAS-QDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIPS-HRVDYLGISWDTD 763 (960)
Q Consensus 711 Dili~s-~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~~~-~~~~fLG~~i~~~ 763 (960)
|++|.- .+..++.+.+..+-..+...|+..+++|.+...+ +.+.|||+.++..
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 999864 5788888888999999999999999999876543 2478999999875
No 54
>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=84.31 E-value=2.3 Score=47.51 Aligned_cols=98 Identities=8% Similarity=-0.067 Sum_probs=66.3
Q ss_pred eccccccccccCcc-ccceEEEEEcCeeEEEEEeCCCCCCHHHHHHHHHHHHHHHHHH--cCCeeeEEecceEEEeCCHH
Q psy15121 356 DLSQAYCHIPIARR-HRRFLCFLYKGTVYQRTCLSFGLASAPQAFAQLSNWVAVLLRE--RGVRCLVYLDDFLLASQDSV 432 (960)
Q Consensus 356 Dl~~~y~qi~l~~~-d~~~taf~~~~~~y~~~~lPfGl~~aP~~fq~~~~~il~~~~~--~~~~~~~YlDDili~s~s~~ 432 (960)
++-..|...|+... |-+-... .-+-.-+|+|-.-||-+-.-+|...-..+.. .|....-|.||++++++ .+
T Consensus 56 ~li~r~L~APl~~~~dg~~~~~-----r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~-~~ 129 (346)
T cd01709 56 DFFKKFLEAPLRFVADGPDAPP-----RIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQ-PE 129 (346)
T ss_pred HHHHHHHhCceeecCCCCcccc-----cccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcC-HH
Confidence 77888888888762 3211111 2233569999999997666666532223322 46778899999999955 56
Q ss_pred HHHHHHHHhhccccccccccCCceecCCcccc
Q psy15121 433 VLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLV 464 (960)
Q Consensus 433 e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~ 464 (960)
+..+....+ -++++..|+++|++|+-.
T Consensus 130 ~a~~aw~~i-----~~fl~~lGLelN~eKT~i 156 (346)
T cd01709 130 TCAKAWKAI-----QEFAKVMGLELNKEKTGS 156 (346)
T ss_pred HHHHHHHHH-----HHHHHHcCceeccccceE
Confidence 666666555 556778899999999654
No 55
>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=83.59 E-value=0.36 Score=52.04 Aligned_cols=111 Identities=16% Similarity=0.196 Sum_probs=65.9
Q ss_pred CcEEEeeehhhccCccccccccccc---ceee--------eeecccccCCCCccccchhhHHHhhHhhhc----------
Q psy15121 643 NDYLATIDLSQAYCHIPIARRHRRF---LCFL--------IPMDMSSFRPSLSSPGVCPTIKLGRRLRER---------- 701 (960)
Q Consensus 643 ~~~fs~lDl~~ay~qI~l~~~d~~~---taF~--------y~~~rlPFG~l~~ap~~f~~~~i~~~l~~~---------- 701 (960)
.-..-.+|++.||-+-+++++ ... .+|. ++..+--+| |+-||..|. ..+...|..+
T Consensus 76 ~~~~~q~Dv~tAfL~~~l~e~-iym~~P~g~~~~~~~~~v~~L~kaLYG-LKQa~r~W~-~~l~~~L~~~GF~~~~~D~c 152 (246)
T PF07727_consen 76 GLELHQMDVKTAFLNGDLDEE-IYMRQPPGFEDPGPPGKVCRLKKALYG-LKQAPRLWY-KTLDKFLKKLGFKQSKADPC 152 (246)
T ss_pred ccccccccccceeeecccccc-hhhccccccccccccccccccccccee-cccccchhh-hhcccccchhhhhccccccc
Confidence 345667899999999988764 211 1111 566667789 999999884 2333333332
Q ss_pred ---------CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCccccccceEEEEEEEEcCCCcEE
Q psy15121 702 ---------GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQIIPSHRVDYLGISWDTDLLQV 767 (960)
Q Consensus 702 ---------~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~~~~~~~fLG~~i~~~g~~~ 767 (960)
...+.+||||++|.+.+.++... +.+.|.+ .+.++ .++. --.|||..+......+
T Consensus 153 lfi~~~~~~~~ii~vYVDDili~~~~~~~i~~----~~~~l~~-~F~iK----dlG~--~~~fLGi~i~~~~~~i 216 (246)
T PF07727_consen 153 LFIKKSGDGFIIILVYVDDILIAGPSEEEIEE----FKKELKK-KFEIK----DLGE--LKYFLGIEIERTKGGI 216 (246)
T ss_pred ccccccccccccccccccccccccccccceec----ccccccc-ccccc----cccc--cccccceEEEECCCEE
Confidence 13466899999999988654432 2233221 12221 1122 3368999887644333
No 56
>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=54.14 E-value=30 Score=37.69 Aligned_cols=61 Identities=25% Similarity=0.258 Sum_probs=45.9
Q ss_pred CCeEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccCcccc---ccceEEEEEEEEcCC
Q psy15121 702 GVRCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKKSQII---PSHRVDYLGISWDTD 763 (960)
Q Consensus 702 ~~~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~~---~~~~~~fLG~~i~~~ 763 (960)
...+++|=||.++..+.. ......+.+.+.+.++|+.++.+|.... ...++.|||+.+...
T Consensus 194 ~~~~~~~GDD~li~~~~~-~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~Fl~r~f~~~ 257 (278)
T cd01699 194 NVRLLNYGDDCLLSVEKA-DDKFNLETLAEWLKEYGLTMTDEDKVESPFRPLEEVEFLKRRFVLD 257 (278)
T ss_pred ceEEEEEcCCeEEEechh-HhhhCHHHHHHHHHHcCCEeCCcccCCCCCCCHhhCcccCCccEEC
Confidence 346789999999988765 3334456677888889999999998752 335889999777643
No 57
>KOG4768|consensus
Probab=33.84 E-value=26 Score=41.68 Aligned_cols=121 Identities=12% Similarity=0.124 Sum_probs=81.5
Q ss_pred cchHhhhhcCCcEEEEeeccccccccccCccccc------------------eEEEEEcCee--EEEEEeCCCCCCHHHH
Q psy15121 339 HQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRR------------------FLCFLYKGTV--YQRTCLSFGLASAPQA 398 (960)
Q Consensus 339 i~~~l~~l~~~~~~s~lDl~~~y~qi~l~~~d~~------------------~taf~~~~~~--y~~~~lPfGl~~aP~~ 398 (960)
+-++...++++.||...||+..|=.||-++==.. -.++++..+. |++.-.|+|---+|-+
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 4566677899999999999999999986542111 1245566655 5577789999999977
Q ss_pred HHHHHHHHHHHHH-----------------------------------------------------HcCCe---eeEEec
Q psy15121 399 FAQLSNWVAVLLR-----------------------------------------------------ERGVR---CLVYLD 422 (960)
Q Consensus 399 fq~~~~~il~~~~-----------------------------------------------------~~~~~---~~~YlD 422 (960)
..-+|+++-+-++ ..|.. .+-|-|
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 6666554433220 11111 357889
Q ss_pred ceEEEeC-CHHHHHHHHHHhhccccccccccCCceecCCcccc
Q psy15121 423 DFLLASQ-DSVVLKNQIFQTLPVNLSGNCSRSGRRSHPTHSLV 464 (960)
Q Consensus 423 Dili~s~-s~~e~~~~l~~~~~~~~~~~l~~~g~~~~~~K~~~ 464 (960)
|++|..- |..+..+.+... -..++..|+.++++|...
T Consensus 509 d~ii~v~GS~nd~K~ilr~I-----n~f~sslGls~n~~kt~i 546 (796)
T KOG4768|consen 509 DIIIGVWGSVNDCKQILRDI-----NNFLSSLGLSNNSSKTQI 546 (796)
T ss_pred CEEEEEeccHHHHHHHHHHH-----HHHHHhhCcccCcccceE
Confidence 9999885 444444444444 446777899999999776
No 58
>KOG1005|consensus
Probab=26.32 E-value=92 Score=38.86 Aligned_cols=77 Identities=18% Similarity=0.113 Sum_probs=52.9
Q ss_pred eeecccccCCCCccccch--hhHHHhh-Hhhh---cCC-eEEEEecceEEecCCHHHHHHHHHHHHHHHHHcCCeecccC
Q psy15121 672 IPMDMSSFRPSLSSPGVC--PTIKLGR-RLRE---RGV-RCLVYLDDFLLASQDPIVLKNQILQTLQLLTYLGWQVNLKK 744 (960)
Q Consensus 672 y~~~rlPFG~l~~ap~~f--~~~~i~~-~l~~---~~~-~v~~YvDDili~s~s~eeh~~~l~~vl~~l~~~Gl~l~~~K 744 (960)
-+-.-+|+| -.-|.-+. -...+.+ .+.. .|. .+..|+||+|+.+.+.++...-++....-..++|+..|.+|
T Consensus 630 vq~~GIpQG-s~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~~~a~kfl~~l~~Gf~~yn~~tn~~K 708 (888)
T KOG1005|consen 630 VQKKGIPQG-SILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTENDQAKKFLKLLSRGFNKYNFFTNEPK 708 (888)
T ss_pred EEecCccCC-CchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCHHHHHHHHHHHhccccccceeccCcc
Confidence 345678999 44443333 1122222 2221 132 56789999999999999999999999899999999999988
Q ss_pred -ccccc
Q psy15121 745 -SQIIP 749 (960)
Q Consensus 745 -~~~~~ 749 (960)
|.|..
T Consensus 709 ~~nF~~ 714 (888)
T KOG1005|consen 709 TVNFEV 714 (888)
T ss_pred cccccc
Confidence 45544
No 59
>PF05869 Dam: DNA N-6-adenine-methyltransferase (Dam); InterPro: IPR008593 This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences [].; GO: 0003677 DNA binding, 0009007 site-specific DNA-methyltransferase (adenine-specific) activity, 0032775 DNA methylation on adenine
Probab=22.96 E-value=77 Score=32.49 Aligned_cols=33 Identities=15% Similarity=0.287 Sum_probs=30.0
Q ss_pred CCCCcccChhhHHHHHhhcCccccccccCCCCC
Q psy15121 183 LIPDWHLLPSLTESVFQRWGIESCAALCDPESP 215 (960)
Q Consensus 183 ~~~~w~l~~~~~~~~~~~wg~~~~d~fa~~~~~ 215 (960)
..++|.-.+.+|..+.+.||+.++|.+|+..+.
T Consensus 10 ~~d~W~TP~~lf~~l~~~fg~f~LD~aa~~~Na 42 (181)
T PF05869_consen 10 DKDEWQTPPELFDALNREFGPFDLDPAASDENA 42 (181)
T ss_pred CCCCCcCCHHHHHHHHHHhCCccccccCCCCCh
Confidence 567999999999999999999999999988664
No 60
>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=20.76 E-value=3.3e+02 Score=32.26 Aligned_cols=135 Identities=20% Similarity=0.209 Sum_probs=0.0
Q ss_pred CCCCeeEE--eec--------------ccccccccCCCCcCCChhhHhhhcCCCcEEEeeehhhccCcccccccccccce
Q psy15121 606 GDGTMRPV--FNL--------------KSLNSYVTTKKFKLINHQKIPLFLQKNDYLATIDLSQAYCHIPIARRHRRFLC 669 (960)
Q Consensus 606 k~gk~R~~--vD~--------------r~LN~~~~~~~~plp~i~~~l~~l~~~~~fs~lDl~~ay~qI~l~~~d~~~ta 669 (960)
+.||.|+. +|| .-|...=....|-....-+.+....+.+.|.++||++|=-..||.-+-+-...
T Consensus 94 ~~gK~Ri~Am~D~~tQ~~L~PlH~~lf~~Lr~ip~DgTF~Q~~~~~~~~~~~~~~~~~S~DLsaATDR~Pi~lQ~~il~~ 173 (498)
T PF05919_consen 94 PEGKVRIFAMVDYWTQCVLKPLHDWLFSILRRIPQDGTFDQEPPFDRLVDSMKEKYFYSFDLSAATDRFPIVLQERILSY 173 (498)
T ss_pred CCCceEEEEEEeHHHHHhhHHHHHHHHHHHhcCCCCCCcCCCCchhhHhhcccCCceEEEeeccccccccHHHHHHHHHH
Q ss_pred ee------------------------eeeccc-ccCCCCccccch--------hhHHHhhHhhhcCCeEEEEecceEEec
Q psy15121 670 FL------------------------IPMDMS-SFRPSLSSPGVC--------PTIKLGRRLRERGVRCLVYLDDFLLAS 716 (960)
Q Consensus 670 F~------------------------y~~~rl-PFG~l~~ap~~f--------~~~~i~~~l~~~~~~v~~YvDDili~s 716 (960)
.. .+|.+= |+| .-+|=++| |..+....-......-..-=|||+|.
T Consensus 174 l~~~~~a~~W~~llv~r~~~~~~~~~v~y~vGQPmG-a~SSW~~~altHH~iV~~aA~~~~~~~~f~~Y~iLGDDivi~- 251 (498)
T PF05919_consen 174 LFGDSFASSWRSLLVGRPYLKPNGDEVRYSVGQPMG-AYSSWAMFALTHHLIVQYAAERVGGGSRFTDYIILGDDIVIA- 251 (498)
T ss_pred HhCchHHHHHHHHHcCCccccCCCCeEEEecCCcch-hccccHHHHhhHHHHHHHHHHHhhccCCCCceEEEcCcEEEc-
Q ss_pred CCHHHHHHHHHHHHHHHHHcCCeecccCccc
Q psy15121 717 QDPIVLKNQILQTLQLLTYLGWQVNLKKSQI 747 (960)
Q Consensus 717 ~s~eeh~~~l~~vl~~l~~~Gl~l~~~K~~~ 747 (960)
+....+.-...+++.|+.++..|+..
T Consensus 252 -----~~~vA~~Y~~~m~~Lgv~is~~Ks~v 277 (498)
T PF05919_consen 252 -----NDKVAKQYLSIMTDLGVEISLSKSHV 277 (498)
T ss_pred -----CHHHHHHHHHHHHHcCceeccCcccc
Done!