Query psy10810
Match_columns 786
No_of_seqs 368 out of 2609
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 19:03:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10810.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10810hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.9 2.4E-21 5.1E-26 180.3 13.7 125 515-640 3-146 (154)
2 PRK06548 ribonuclease H; Provi 99.8 1.8E-20 3.9E-25 178.2 12.7 123 514-641 4-144 (161)
3 PRK00203 rnhA ribonuclease H; 99.8 5.6E-20 1.2E-24 175.8 13.1 123 515-641 3-144 (150)
4 PRK08719 ribonuclease H; Revie 99.8 5.5E-20 1.2E-24 173.8 12.4 119 514-638 3-146 (147)
5 cd01651 RT_G2_intron RT_G2_int 99.8 1.4E-20 3.1E-25 193.6 8.5 153 14-251 39-215 (226)
6 cd03487 RT_Bac_retron_II RT_Ba 99.8 4.5E-20 9.8E-25 187.8 11.0 157 14-286 31-198 (214)
7 cd01650 RT_nLTR_like RT_nLTR: 99.8 4.7E-20 1E-24 188.9 8.4 167 7-283 39-220 (220)
8 PF00078 RVT_1: Reverse transc 99.8 1.5E-20 3.2E-25 191.4 3.2 170 12-283 34-214 (214)
9 PF00075 RNase_H: RNase H; In 99.8 2.7E-19 5.8E-24 167.9 10.8 118 514-637 2-131 (132)
10 cd01646 RT_Bac_retron_I RT_Bac 99.7 3.6E-17 7.8E-22 158.2 6.3 143 44-286 1-147 (158)
11 cd01709 RT_like_1 RT_like_1: A 99.7 6.5E-16 1.4E-20 161.2 15.6 173 44-300 27-211 (346)
12 KOG3752|consensus 99.7 4.6E-16 9.9E-21 161.7 12.7 126 514-639 211-365 (371)
13 cd06222 RnaseH RNase H (RNase 99.6 3.4E-15 7.5E-20 137.9 13.9 120 517-637 1-130 (130)
14 PRK13907 rnhA ribonuclease H; 99.6 1.6E-14 3.6E-19 134.5 13.6 118 516-638 2-126 (128)
15 KOG4768|consensus 99.6 3E-15 6.5E-20 161.8 9.5 287 12-340 328-644 (796)
16 cd01648 TERT TERT: Telomerase 99.5 9.6E-15 2.1E-19 133.8 6.6 104 159-284 8-119 (119)
17 PRK07708 hypothetical protein; 99.5 1.4E-13 3E-18 138.5 14.5 128 512-643 70-212 (219)
18 PRK07238 bifunctional RNase H/ 99.3 5.2E-11 1.1E-15 131.7 15.0 121 515-640 2-133 (372)
19 cd00304 RT_like RT_like: Rever 99.2 5.9E-11 1.3E-15 104.9 7.3 71 171-248 12-85 (98)
20 PF13456 RVT_3: Reverse transc 98.9 4.9E-09 1.1E-13 90.2 9.7 82 552-638 1-86 (87)
21 KOG1005|consensus 98.8 2.1E-08 4.6E-13 114.1 10.7 122 152-286 615-743 (888)
22 cd03714 RT_DIRS1 RT_DIRS1: Rev 98.5 2.4E-07 5.3E-12 85.0 7.0 72 170-247 33-106 (119)
23 cd01645 RT_Rtv RT_Rtv: Reverse 98.4 3.4E-07 7.4E-12 93.1 4.9 72 169-246 127-201 (213)
24 cd01648 TERT TERT: Telomerase 98.2 8.5E-07 1.9E-11 81.2 2.1 47 100-146 17-70 (119)
25 cd03715 RT_ZFREV_like RT_ZFREV 98.0 7.1E-06 1.5E-10 83.3 4.7 74 168-247 122-198 (210)
26 cd03487 RT_Bac_retron_II RT_Ba 97.4 8.3E-05 1.8E-09 75.7 3.3 56 103-158 104-167 (214)
27 cd01709 RT_like_1 RT_like_1: A 97.1 0.00048 1E-08 73.1 4.3 58 101-158 82-142 (346)
28 cd01647 RT_LTR RT_LTR: Reverse 97.0 0.00085 1.8E-08 65.3 5.2 72 169-247 94-165 (177)
29 cd01651 RT_G2_intron RT_G2_int 97.0 0.0004 8.7E-09 71.1 2.8 56 101-156 125-195 (226)
30 COG3344 Retron-type reverse tr 96.8 0.001 2.2E-08 72.5 4.0 106 12-127 144-263 (328)
31 cd01646 RT_Bac_retron_I RT_Bac 96.8 0.0007 1.5E-08 65.4 2.3 59 100-158 51-113 (158)
32 cd00304 RT_like RT_like: Rever 96.0 0.005 1.1E-07 53.9 2.9 43 103-145 12-57 (98)
33 PF00078 RVT_1: Reverse transc 95.9 0.004 8.7E-08 62.8 2.1 47 100-146 123-173 (214)
34 cd01699 RNA_dep_RNAP RNA_dep_R 95.6 0.039 8.4E-07 58.5 8.4 76 165-247 154-238 (278)
35 PF13966 zf-RVT: zinc-binding 94.4 0.021 4.6E-07 48.9 1.7 31 718-748 51-82 (86)
36 cd01650 RT_nLTR_like RT_nLTR: 94.3 0.034 7.4E-07 56.5 3.2 45 102-146 110-159 (220)
37 cd01644 RT_pepA17 RT_pepA17: R 93.5 0.057 1.2E-06 54.8 3.2 68 168-241 101-173 (213)
38 KOG4768|consensus 88.6 0.29 6.2E-06 55.2 2.6 30 164-193 411-440 (796)
39 KOG1005|consensus 75.8 2.7 5.8E-05 49.7 3.9 69 70-144 608-682 (888)
40 PF09004 DUF1891: Domain of un 69.7 0.71 1.5E-05 33.3 -1.6 41 289-331 1-41 (42)
41 PF05380 Peptidase_A17: Pao re 65.9 22 0.00049 34.1 7.3 55 513-569 79-143 (159)
42 COG3344 Retron-type reverse tr 62.3 13 0.00027 40.5 5.5 48 164-211 232-281 (328)
43 CHL00002 matK maturase K 61.1 16 0.00034 41.9 5.9 54 194-252 270-324 (504)
44 cd01645 RT_Rtv RT_Rtv: Reverse 55.3 6.2 0.00013 40.0 1.4 45 101-145 127-174 (213)
45 PF00336 DNA_pol_viral_C: DNA 52.4 17 0.00037 35.7 3.7 90 513-620 92-183 (245)
46 cd03714 RT_DIRS1 RT_DIRS1: Rev 40.1 19 0.00041 32.5 2.0 43 102-144 33-76 (119)
47 PF03431 RNA_replicase_B: RNA 40.0 88 0.0019 35.0 7.2 43 41-92 246-289 (542)
48 PF05919 Mitovir_RNA_pol: Mito 38.0 1.9E+02 0.0041 32.9 9.5 42 41-84 150-192 (498)
49 PF05741 zf-nanos: Nanos RNA b 35.7 18 0.00038 28.0 0.9 21 727-747 34-54 (55)
50 PHA00028 rep RNA replicase, be 33.6 80 0.0017 35.8 5.7 40 194-246 331-370 (561)
51 PF00680 RdRP_1: RNA dependent 31.7 44 0.00095 38.5 3.7 79 162-247 297-388 (491)
52 COG3341 Predicted double-stran 28.1 1.3E+02 0.0029 30.1 5.7 93 549-643 105-205 (225)
53 PF07727 RVT_2: Reverse transc 22.4 45 0.00098 34.6 1.4 41 170-214 123-180 (246)
54 cd01644 RT_pepA17 RT_pepA17: R 22.1 60 0.0013 32.9 2.2 45 102-146 103-152 (213)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.86 E-value=2.4e-21 Score=180.28 Aligned_cols=125 Identities=28% Similarity=0.371 Sum_probs=103.2
Q ss_pred cEEEEecCCC-C-CCCeeEEEEeCCC-cceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhcc
Q psy10810 515 HIKIYTDGSK-N-EQGVGCALTIPEK-NIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNM 591 (786)
Q Consensus 515 ~~~iytDGS~-~-~~~~G~a~~~~~~-~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~ 591 (786)
.+.||||||+ + +|..|+|+++..+ ......+....+||++||++|++.||+++.+.+.+.|.|+|||++++++|..|
T Consensus 3 ~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w 82 (154)
T COG0328 3 KVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRW 82 (154)
T ss_pred ceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHH
Confidence 5789999999 3 4457888887533 33323333338999999999999999999988899999999999999999975
Q ss_pred CCC----------------cHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhcCC
Q psy10810 592 FHE----------------NPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINND 640 (786)
Q Consensus 592 ~~~----------------~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~~ 640 (786)
..+ .++|+++.+++.++ ..|.+.|||||+|.++||.||+||+.|++..
T Consensus 83 ~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~-~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 83 IVKWKKNGWKTADKKPVKNKDLWEELDELLKRH-ELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HhhccccCccccccCccccHHHHHHHHHHHhhC-CeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 322 25799988888764 4899999999999999999999999998765
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.84 E-value=1.8e-20 Score=178.18 Aligned_cols=123 Identities=28% Similarity=0.296 Sum_probs=97.3
Q ss_pred CcEEEEecCCCC--CCCeeEEEEeCCCcceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhc-
Q psy10810 514 SHIKIYTDGSKN--EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITN- 590 (786)
Q Consensus 514 ~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~- 590 (786)
..+.||||||+. ++..|+|+++.+.. ...+....+||++|||.|++.||+.+.. ...++.|+|||++|++++..
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~--~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W 80 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENT--WDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKW 80 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCc--EEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHH
Confidence 458999999993 34578998875432 2233345789999999999999986643 34679999999999999994
Q ss_pred --------cCC-------CcHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhcCCC
Q psy10810 591 --------MFH-------ENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINNDV 641 (786)
Q Consensus 591 --------~~~-------~~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~~~ 641 (786)
|.. +.++|++|.+++.. ..|.|.|||||+|++|||.||+||++|+....
T Consensus 81 ~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~ 144 (161)
T PRK06548 81 VYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIRMSWVNAHTGHPLNEAADSLARQAANNFS 144 (161)
T ss_pred HHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence 322 23688999888875 37999999999999999999999999986543
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.82 E-value=5.6e-20 Score=175.76 Aligned_cols=123 Identities=27% Similarity=0.372 Sum_probs=97.4
Q ss_pred cEEEEecCCCC-C-CCeeEEEEeCC-CcceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhcc
Q psy10810 515 HIKIYTDGSKN-E-QGVGCALTIPE-KNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNM 591 (786)
Q Consensus 515 ~~~iytDGS~~-~-~~~G~a~~~~~-~~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~ 591 (786)
.+.||||||+. + +..|+|+++.. +......+.....|+++|||.|++.||+.+.+ ...+.|+|||++++++|..|
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence 48899999994 3 44788887632 22323334445789999999999999998865 56899999999999999863
Q ss_pred CC----------------CcHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhcCCC
Q psy10810 592 FH----------------ENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINNDV 641 (786)
Q Consensus 592 ~~----------------~~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~~~ 641 (786)
.. +.+++++|.+++.. ..|.|.|||||+|++||+.||+||++|+..+.
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 21 13578888887764 68999999999999999999999999987653
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.82 E-value=5.5e-20 Score=173.76 Aligned_cols=119 Identities=28% Similarity=0.384 Sum_probs=92.0
Q ss_pred CcEEEEecCCCCC-C----CeeEEEEeCC--Ccc--eEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHH
Q psy10810 514 SHIKIYTDGSKNE-Q----GVGCALTIPE--KNI--AKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSC 584 (786)
Q Consensus 514 ~~~~iytDGS~~~-~----~~G~a~~~~~--~~~--~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a 584 (786)
..++||||||+.. + .+|+|+++.. +.. .....+....|+++||+.|++.||+.+.+ ...|+|||+++
T Consensus 3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~----~~~i~tDS~yv 78 (147)
T PRK08719 3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARD----GDVIYSDSDYC 78 (147)
T ss_pred ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCC----CCEEEechHHH
Confidence 4689999999932 2 2588887632 232 23344556689999999999999999865 24899999999
Q ss_pred HHHHhc---------cCC-------CcHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhc
Q psy10810 585 LQAITN---------MFH-------ENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAIN 638 (786)
Q Consensus 585 ~~~l~~---------~~~-------~~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~ 638 (786)
+++++. |.. +.++++.|.++.. ...|.|.|||||+|++|||.||+||++|++
T Consensus 79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 999853 221 1357888777766 357999999999999999999999999975
No 5
>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=99.82 E-value=1.4e-20 Score=193.60 Aligned_cols=153 Identities=18% Similarity=0.269 Sum_probs=122.2
Q ss_pred cccCcchhhccccCcchhhhcccc---------ccccceec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCe
Q psy10810 14 NHLNDLTIKLRDINPKIICIQESH---------LKEEENFT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRS 83 (786)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~ 83 (786)
..+++.||| |+|++++.++.. ......+| ++|||+|+|+. |++.|+..+.++.++.++.+++....
T Consensus 39 ~~~~~~~~g---~~~~rs~~~~i~~i~~~~~~~~~~~~~~Di~~~Fdsi~~~~-l~~~l~~~~~~~~~~~~i~~~~~~~~ 114 (226)
T cd01651 39 PRFSDCSYG---FRPGRSAHDALKAIRRNVKGGYTWVIEGDIKGFFDNIDHDL-LLKILKRRIGDKRVLRLIRKWLKAGV 114 (226)
T ss_pred hccccCCCC---CCCCCCHHHHHHHHHHHhcCCCeEEEEccHHHhcCCCCHHH-HHHHHHHhcccHHHHHHHHHHHhceE
Confidence 557889999 999999987722 12223479 99999999999 99999999999999999999864321
Q ss_pred eEEEECCceeecceecccccCCCccccchhHHHHHHhhhhhcccccccccccccchhhccccchhHHHHHHhhhcccccc
Q psy10810 84 FKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSE 163 (786)
Q Consensus 84 ~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~s~ 163 (786)
. .+ +.
T Consensus 115 ~---~~------------------------------------------------------------------------~~ 119 (226)
T cd01651 115 L---ED------------------------------------------------------------------------GK 119 (226)
T ss_pred c---cC------------------------------------------------------------------------Ce
Confidence 1 11 22
Q ss_pred ceeeecCcCCCCcchHHHHHHHhhcccccc--------------CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHH
Q psy10810 164 DFSIVCGIPQGGVVSGTLFAIAINSITSYI--------------HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKL 229 (786)
Q Consensus 164 ~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~--------------~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l 229 (786)
......|+|||+++||+||++|++++...+ ...+...+||||+++++.+.+. ++.+++.+
T Consensus 120 ~~~~~~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~------~~~~~~~i 193 (226)
T cd01651 120 LVETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKE------AEEIKELI 193 (226)
T ss_pred EeCCCCCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHH------HHHHHHHH
Confidence 334567888888888888888888776655 1668899999999999887543 78899999
Q ss_pred HHHHhhcCCccCCCCeeEEEec
Q psy10810 230 ENFSNDTGLFFSPQKSQCVLFS 251 (786)
Q Consensus 230 ~~w~~~~gL~ln~~KT~~~~f~ 251 (786)
.+|++..||.+|++||++++++
T Consensus 194 ~~~~~~~gl~ln~~Kt~i~~~~ 215 (226)
T cd01651 194 REFLEELGLELNPEKTRITHFK 215 (226)
T ss_pred HHHHHHcCCeechhhcceeecC
Confidence 9999999999999999998874
No 6
>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=99.82 E-value=4.5e-20 Score=187.82 Aligned_cols=157 Identities=13% Similarity=0.143 Sum_probs=122.3
Q ss_pred cccCcchhhccccCcchhhhccccc----cccceec-ccccccccchHHHHHHHHhccCC-CChHHHHHhhhCCCeeEEE
Q psy10810 14 NHLNDLTIKLRDINPKIICIQESHL----KEEENFT-LKGFNTVGTYEVILRQLHKWNMR-GHLPIFLSKYMDPRSFKIR 87 (786)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ld-~~AFD~V~~~~~L~~~L~~~g~~-~~~~~~i~~~l~~r~~~v~ 87 (786)
..+++.++| |+|+++++++... ...+.+| ++|||+|+|+. |++.|...|.+ +.+..++..++..
T Consensus 31 ~~~~~~~~g---~~~grs~~~~~~~~~~~~~v~~~Di~~fFdsI~~~~-L~~~l~~~~~~~~~~~~~l~~~~~~------ 100 (214)
T cd03487 31 LPVHDAAHG---FVKGRSIITNAKPHCGAKYVLKLDIKDFFPSITFER-VRGVFRSLGYFSPDVATILAKLCTY------ 100 (214)
T ss_pred CCCCcceee---ecCCCCHHHHHHHhcCCCEEEEeehhhhcccCCHHH-HHHHHHHcCCCCHHHHHHHHHHHhC------
Confidence 346789999 9999999887432 2233479 99999999999 99999999998 6667776665421
Q ss_pred ECCceeecceecccccCCCccccchhHHHHHHhhhhhcccccccccccccchhhccccchhHHHHHHhhhccccccceee
Q psy10810 88 LNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSEDFSI 167 (786)
Q Consensus 88 ~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~s~~~~~ 167 (786)
T Consensus 101 -------------------------------------------------------------------------------- 100 (214)
T cd03487 101 -------------------------------------------------------------------------------- 100 (214)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ecCcCCCCcchHHHHHHHhhcccccc-----CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCC
Q psy10810 168 VCGIPQGGVVSGTLFAIAINSITSYI-----HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSP 242 (786)
Q Consensus 168 ~~GvpQGs~LSPlLF~l~~~~l~~~~-----~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~ 242 (786)
..|+|||+|+||+|||+|++++...+ ..++.+.+||||++|++.+... ..++++++.+..|+.+.||.+|+
T Consensus 101 ~~GlpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~----~~~~~~~~~i~~~l~~~gL~ln~ 176 (214)
T cd03487 101 NGHLPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLK----EALDKLLEIIRSILSEEGFKINK 176 (214)
T ss_pred CCCcCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccch----hHHHHHHHHHHHHHHHCCceeCC
Confidence 13777777777777777777766554 3467899999999998877542 34789999999999999999999
Q ss_pred CCeeEEEecccCcCCCcceeeecCCceeeeecceEEeeeEecCC
Q psy10810 243 QKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTFDKK 286 (786)
Q Consensus 243 ~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~id~~ 286 (786)
+||+++..+ ..+.+||+.+.+.
T Consensus 177 ~Kt~i~~~~----------------------~~~~~~G~~i~~~ 198 (214)
T cd03487 177 SKTRISSKG----------------------SRQIVTGLVVNNG 198 (214)
T ss_pred CceEEccCC----------------------CCcEEEEEEEeCC
Confidence 999987642 3457999999764
No 7
>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=99.80 E-value=4.7e-20 Score=188.94 Aligned_cols=167 Identities=27% Similarity=0.425 Sum_probs=126.6
Q ss_pred hhhhccccccCcchhhccccCcchhhhccccc--------------cccceec-ccccccccchHHHHHHHHhccCCCCh
Q psy10810 7 WNVNGVKNHLNDLTIKLRDINPKIICIQESHL--------------KEEENFT-LKGFNTVGTYEVILRQLHKWNMRGHL 71 (786)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~ld-~~AFD~V~~~~~L~~~L~~~g~~~~~ 71 (786)
++-.-+...+.+.|+| |++++++.++... ...+.+| ++|||+|+|+. |++.|
T Consensus 39 ~l~~~~~~~~~~~q~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~Di~~aFdsi~~~~-l~~~l--------- 105 (220)
T cd01650 39 RLRPVLEENILPNQFG---FRPGRSTTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEF-LLKAL--------- 105 (220)
T ss_pred HHHHHHhhcCCccccc---ccCCChHHHHHHHHHHHHHHHHHcCCceEEEEEEHHhhcCcCCHHH-HHHHh---------
Confidence 3344445666789999 9999998666211 2334579 99999999999 99988
Q ss_pred HHHHHhhhCCCeeEEEECCceeecceecccccCCCccccchhHHHHHHhhhhhcccccccccccccchhhccccchhHHH
Q psy10810 72 PIFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLV 151 (786)
Q Consensus 72 ~~~i~~~l~~r~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~ 151 (786)
|+|||+++||+||+++++.++..+.....
T Consensus 106 ------------------------------GipQG~~lSp~l~~l~~~~l~~~~~~~~~--------------------- 134 (220)
T cd01650 106 ------------------------------GVRQGDPLSPLLFNLALDDLLRLLNKEEE--------------------- 134 (220)
T ss_pred ------------------------------CCccCCcccHHHHHHHHHHHHHHHHhhcc---------------------
Confidence 67888888888888888877655544210
Q ss_pred HHHhhhccccccceeeecCcCCCCcchHHHHHHHhhccccccCCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHH
Q psy10810 152 SIMQESIDTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLEN 231 (786)
Q Consensus 152 ~~l~~~~~~~s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~ 231 (786)
.......+...+||||+++++.+.. ..++..++.+.+
T Consensus 135 --------------------------------------~~~~~~~~~~~~yaDD~~i~~~~~~-----~~~~~~~~~~~~ 171 (220)
T cd01650 135 --------------------------------------IKLGGPGITHLAYADDIVLFSEGKS-----RKLQELLQRLQE 171 (220)
T ss_pred --------------------------------------ccCCCCccceEEeccceeeeccCCH-----HHHHHHHHHHHH
Confidence 0001346789999999999988765 358999999999
Q ss_pred HHhhcCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEeeeEe
Q psy10810 232 FSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTF 283 (786)
Q Consensus 232 w~~~~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i 283 (786)
|+..+|+++|++||++++++...... ..+... +..+.....+||||++|
T Consensus 172 ~~~~~gl~in~~Kt~~~~~~~~~~~~-~~~~~~--~~~~~~~~~~kyLG~~i 220 (220)
T cd01650 172 WSKESGLKINPSKSKVMLIGNKKKRL-KDITLN--GTPIEAVETFKYLGVTI 220 (220)
T ss_pred HHHHcCCEEChhheEEEEecCCCcch-hhhhhc--CCcccCCCCCeeccccC
Confidence 99999999999999999998776542 223344 88888999999999875
No 8
>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=99.80 E-value=1.5e-20 Score=191.39 Aligned_cols=170 Identities=22% Similarity=0.421 Sum_probs=137.3
Q ss_pred cccccCcchhhccccCcchhhhc-----c-ccccccceec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCee
Q psy10810 12 VKNHLNDLTIKLRDINPKIICIQ-----E-SHLKEEENFT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRSF 84 (786)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~-----~-~~~~~~~~ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~~ 84 (786)
+.+++.+.++| |+++++|++ . ........+| ++|||+|+|+. +.+.|...+.++.++.|+.+++.++..
T Consensus 34 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~Di~~~f~sI~~~~-l~~~l~~~~~~~~~~~~i~~~~~~~~~ 109 (214)
T PF00078_consen 34 LEPIFSPSQFG---FRPGRSCHDIKKLNRFKGYLYFLKLDISKAFDSIPHHR-LLRKLKRFGVPKKLIRLIQNLLSDRTA 109 (214)
T ss_dssp ----HHHTTSS---CSHGCCCHHHHHHHC-CGSSEEEEEECCCCGGGSBBHT-TTGGGGEEEEECCSCHHHHHHHHHHHH
T ss_pred ccccCCCCCCC---Ccccccccccccccccccccccceeccccccccceeee-ccccccccccccccccccccccccccc
Confidence 35668999999 999999855 1 2223333579 99999999999 999999999999999999999999888
Q ss_pred EEEECCceeecceecccccCCCccccchhHHHHHHhhhhhcccccccccccccchhhccccchhHHHHHHhhhccccccc
Q psy10810 85 KIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSED 164 (786)
Q Consensus 85 ~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~s~~ 164 (786)
.+.+++. . ..
T Consensus 110 ~~~~~~~---------------------------------------------------------------------~-~~ 119 (214)
T PF00078_consen 110 KVYLDGD---------------------------------------------------------------------L-SP 119 (214)
T ss_dssp -EECGCS---------------------------------------------------------------------S-SE
T ss_pred ccccccc---------------------------------------------------------------------c-cc
Confidence 8887651 1 34
Q ss_pred eeeecCcCCCCcchHHHHHHHhhcccccc-C---CCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy10810 165 FSIVCGIPQGGVVSGTLFAIAINSITSYI-H---PSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFF 240 (786)
Q Consensus 165 ~~~~~GvpQGs~LSPlLF~l~~~~l~~~~-~---~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~l 240 (786)
.....|+|||+++||+||++|++++.+.+ . +++.+..||||+++++.+.. .+++.++.+.+|++++||++
T Consensus 120 ~~~~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~------~~~~~~~~i~~~~~~~gl~l 193 (214)
T PF00078_consen 120 YFQKRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYADDILIISKSKE------ELQKILEKISQWLEELGLKL 193 (214)
T ss_dssp EEEESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHH------HHHHHHHHHHHHHHHTTSBC
T ss_pred ccccccccccccccchhhccccccccccccccccccccceEeccccEEEECCHH------HHHHHHHHHHHHHHHCCCEE
Confidence 56678999999999999999999988876 2 67899999999999988633 38999999999999999999
Q ss_pred CCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEeeeEe
Q psy10810 241 SPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTF 283 (786)
Q Consensus 241 n~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~i 283 (786)
|++||++++ ..+.++|||+.|
T Consensus 194 n~~Kt~~~~----------------------~~~~~~~lG~~i 214 (214)
T PF00078_consen 194 NPEKTKILH----------------------PSDSVKFLGYVI 214 (214)
T ss_dssp SSTTTSCS------------------------ESSEEETTEEE
T ss_pred ChHHEEEEe----------------------CCCCEEEEeEEC
Confidence 999998653 457789999875
No 9
>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=99.79 E-value=2.7e-19 Score=167.87 Aligned_cols=118 Identities=35% Similarity=0.445 Sum_probs=92.2
Q ss_pred CcEEEEecCCCC--CCCeeEEEEeCCCcceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhc-
Q psy10810 514 SHIKIYTDGSKN--EQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITN- 590 (786)
Q Consensus 514 ~~~~iytDGS~~--~~~~G~a~~~~~~~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~- 590 (786)
..+.||||||+. ++..|+|++++.+. .....++ ..+++.||+.||..||+.+ . ..++.|+|||+++++.+..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~-~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~ 76 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGR-NFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKW 76 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTE-EEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCe-EEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHh
Confidence 468999999973 34467777665442 3333444 8999999999999999944 3 4999999999999998877
Q ss_pred -----cCCC--c-HHHHHHHHHHhcCCCcEEEEEecCCCCC-CcchHHhHHHHHHh
Q psy10810 591 -----MFHE--N-PLVKRVQEELSSIEPSIEFLWCPSHVGI-AGNEAADEEAKQAI 637 (786)
Q Consensus 591 -----~~~~--~-~~~~~i~~~~~~~~~~v~~~wvpgH~g~-~~Ne~AD~lAk~a~ 637 (786)
+... . ++..+|.+++.. +..|.|+|||||+|+ .|||.||+|||+|+
T Consensus 77 ~~~~~~~~~~~~~~i~~~i~~~~~~-~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 77 LHGNGWKKTSNGRPIKNEIWELLSR-GIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHTTSBSCTSSSBHTHHHHHHHHH-SSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred ccccccccccccccchhheeecccc-ceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 2111 2 477788887744 789999999999999 69999999999997
No 10
>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=99.68 E-value=3.6e-17 Score=158.23 Aligned_cols=143 Identities=21% Similarity=0.280 Sum_probs=111.9
Q ss_pred ec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCeeEEEECCceeecceecccccCCCccccchhHHHHHHhhh
Q psy10810 44 FT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSIT 122 (786)
Q Consensus 44 ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~ 122 (786)
+| ++|||+|+|+. |++.|...+.+...+.+++.+..... +.
T Consensus 1 lDi~~fF~sI~~~~-l~~~l~~~~~~~~~~~~~~~~~~~~~-----~~-------------------------------- 42 (158)
T cd01646 1 LDISNFYDSIYTHS-LPWALHGKIKAKQLLKLLRLLGNLLD-----LL-------------------------------- 42 (158)
T ss_pred CchhhccCcchHHH-HHHHHHhhhhhHhhhhhHHHHHHHHH-----HH--------------------------------
Confidence 58 99999999999 99999999999998888743332100 00
Q ss_pred hhcccccccccccccchhhccccchhHHHHHHhhhccccccceeeecCcCCCCcchHHHHHHHhhcccccc---CCCCce
Q psy10810 123 SYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYI---HPSLSS 199 (786)
Q Consensus 123 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~---~~~~~~ 199 (786)
..+.......|+|||+++||+|+++++.++...+ ...+..
T Consensus 43 -------------------------------------~~~~~~~~~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~ 85 (158)
T cd01646 43 -------------------------------------LLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDY 85 (158)
T ss_pred -------------------------------------HHhccCCCCceEccCcchHHHHHHHHHHHHHHHHHhccCCceE
Confidence 0012234468999999999999999999987766 368899
Q ss_pred eeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEe
Q psy10810 200 SLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFL 279 (786)
Q Consensus 200 ~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyL 279 (786)
.+||||+++++.+.. .++++++.+.+|+++.||.+|++||++++++... ..+.+|
T Consensus 86 ~RY~DD~~i~~~~~~------~~~~~~~~i~~~l~~~gL~ln~~Kt~~~~~~~~~-------------------~~~~fl 140 (158)
T cd01646 86 VRYVDDIRIFADSKE------EAEEILEELKEFLAELGLSLNLSKTEILPLPEGT-------------------ASKDFL 140 (158)
T ss_pred EEecCcEEEEcCCHH------HHHHHHHHHHHHHHHCCCEEChhhceeeecCCCC-------------------cccccc
Confidence 999999999987533 3688999999999999999999999998864321 456789
Q ss_pred eeEecCC
Q psy10810 280 GLTFDKK 286 (786)
Q Consensus 280 Gv~id~~ 286 (786)
|..+...
T Consensus 141 g~~~~~~ 147 (158)
T cd01646 141 GYRFSPI 147 (158)
T ss_pred ceEeehh
Confidence 9888654
No 11
>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=99.67 E-value=6.5e-16 Score=161.17 Aligned_cols=173 Identities=14% Similarity=0.147 Sum_probs=117.1
Q ss_pred ec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCeeEEEECCceeecceecccccCCCccccchhHHHHHHhhh
Q psy10810 44 FT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSIT 122 (786)
Q Consensus 44 ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~ 122 (786)
.| ++.||+|+|+. |+..|+.+|++.+++.+|+.||+..-..+ -+|..
T Consensus 27 ~Dik~fFdsIpH~~-Lm~vL~~~~~~~~wL~li~r~L~APl~~~-~dg~~------------------------------ 74 (346)
T cd01709 27 SDFKWFGPSLPHST-ILAVLKFFGVPEKWLDFFKKFLEAPLRFV-ADGPD------------------------------ 74 (346)
T ss_pred eehHhhCCCCCHHH-HHHHHHHhCCCHHHHHHHHHHHhCceeec-CCCCc------------------------------
Confidence 46 99999999999 99999999999999999999997432221 12200
Q ss_pred hhcccccccccccccchhhccccchhHHHHHHhhhccccccceeeecCcCCCCcchHHHHHHHhhcccccc---CCCCce
Q psy10810 123 SYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYI---HPSLSS 199 (786)
Q Consensus 123 ~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~---~~~~~~ 199 (786)
+....-.+|+|||+++||+|-|+|++.+...+ .++..+
T Consensus 75 ---------------------------------------~~~r~r~rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l 115 (346)
T cd01709 75 ---------------------------------------APPRIRKRGTPMSHALSDVFGELVLFCLDFAVNQATDGGLL 115 (346)
T ss_pred ---------------------------------------ccccccCCccCCCchhhHHHHHHHHHHHHHHHHhcCCCceE
Confidence 11122346777777777777777777554444 357889
Q ss_pred eeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEe
Q psy10810 200 SLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFL 279 (786)
Q Consensus 200 ~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyL 279 (786)
.+||||++++... ++...+...+.++++..||++|++||.++.+....+..+..+ ...-|...++|-
T Consensus 116 ~RYaDD~vi~~~~-------~~a~~aw~~i~~fl~~lGLelN~eKT~iV~~~~~~r~~~~~~------~~~LP~g~i~wg 182 (346)
T cd01709 116 YRLHDDLWFWGQP-------ETCAKAWKAIQEFAKVMGLELNKEKTGSVYLSDDTKTRDTTI------DATLPEGPVRWG 182 (346)
T ss_pred EEEcCeEEEEcCH-------HHHHHHHHHHHHHHHHcCceeccccceEEEeccCCccCCCcc------cccCCCCCceee
Confidence 9999999999432 235677778899999999999999999998875543211111 111134456665
Q ss_pred eeEecCC-Cch-------HHHHHHHHHHH
Q psy10810 280 GLTFDKK-MTW-------KVHLKNLKQSC 300 (786)
Q Consensus 280 Gv~id~~-l~~-------~~hi~~~~~ka 300 (786)
=..+|+. .+| +.||+++.+..
T Consensus 183 fL~Ld~~~G~~~Idq~~Vd~hi~el~~QL 211 (346)
T cd01709 183 FLKLDPKTGRWEIDQSQVDAHIDELRKQL 211 (346)
T ss_pred eEEecCCCCcEEeeHHHHHHHHHHHHHHh
Confidence 5566654 333 45555544433
No 12
>KOG3752|consensus
Probab=99.66 E-value=4.6e-16 Score=161.66 Aligned_cols=126 Identities=22% Similarity=0.217 Sum_probs=102.3
Q ss_pred CcEEEEecCCC-CC----CCeeEEEEeCCCcce-EEecCC-CCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHH
Q psy10810 514 SHIKIYTDGSK-NE----QGVGCALTIPEKNIA-KRFGLN-KNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQ 586 (786)
Q Consensus 514 ~~~~iytDGS~-~~----~~~G~a~~~~~~~~~-~~~~~~-~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~ 586 (786)
+..++|||||+ .+ ..+|+|++.+++.+. ....+. +.+++++|||.|+..||+-|.+.+..+++|.|||+++++
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~ 290 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFIN 290 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHH
Confidence 45899999999 32 348999999666443 444554 789999999999999999999988889999999999999
Q ss_pred HHhccCCCc---------------------HHHHHHHHHHhc-CCCcEEEEEecCCCCCCcchHHhHHHHHHhcC
Q psy10810 587 AITNMFHEN---------------------PLVKRVQEELSS-IEPSIEFLWCPSHVGIAGNEAADEEAKQAINN 639 (786)
Q Consensus 587 ~l~~~~~~~---------------------~~~~~i~~~~~~-~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~ 639 (786)
+|+.|..++ +...++.++.+. .+.+|.+.|||||.|+.|||+||.||++++..
T Consensus 291 ~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 291 SLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 999865442 244455555554 46899999999999999999999999998643
No 13
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=99.63 E-value=3.4e-15 Score=137.92 Aligned_cols=120 Identities=35% Similarity=0.446 Sum_probs=95.9
Q ss_pred EEEecCCCCC--CCeeEEEEeCCC--cce-EEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhcc
Q psy10810 517 KIYTDGSKNE--QGVGCALTIPEK--NIA-KRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNM 591 (786)
Q Consensus 517 ~iytDGS~~~--~~~G~a~~~~~~--~~~-~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~ 591 (786)
.+|||||... +++|+|+++... ... .........+++.+|+.|+..||+.+...+..++.|++||+.++..++++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~ 80 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW 80 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence 4899999954 468888887432 222 22222257899999999999999999988899999999999999999986
Q ss_pred CC-----CcHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHh
Q psy10810 592 FH-----ENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAI 637 (786)
Q Consensus 592 ~~-----~~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~ 637 (786)
.. ...+++++.+.+. ....+.|.|||+|+|+++|+.||.||++|.
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~-~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLK-RFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred ccCCChhhHHHHHHHHHHHh-CCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 43 1246667777663 357899999999999999999999999874
No 14
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.59 E-value=1.6e-14 Score=134.50 Aligned_cols=118 Identities=26% Similarity=0.265 Sum_probs=92.7
Q ss_pred EEEEecCCCC--CCCeeEEEEeCCCc-ceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhccC
Q psy10810 516 IKIYTDGSKN--EQGVGCALTIPEKN-IAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNMF 592 (786)
Q Consensus 516 ~~iytDGS~~--~~~~G~a~~~~~~~-~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~~ 592 (786)
+.||||||+. ++..|+|+++.+.. .....+....++++.||+.|++.||+.+.+.+...+.|+|||+.+++.+++..
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~ 81 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY 81 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence 6799999993 35688998874322 21222233568999999999999999999988889999999999999998833
Q ss_pred C----CcHHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhc
Q psy10810 593 H----ENPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAIN 638 (786)
Q Consensus 593 ~----~~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~ 638 (786)
. ..++++++..++.+. ..+.+.|||. +.|+.||.||++|..
T Consensus 82 ~~~~~~~~l~~~~~~l~~~f-~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 82 AKNKMFAPLLEEALQYIKSF-DLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred hcChhHHHHHHHHHHHHhcC-CceEEEEcCc----hhchhHHHHHHHHHh
Confidence 2 246778887777653 5677899995 689999999999974
No 15
>KOG4768|consensus
Probab=99.59 E-value=3e-15 Score=161.82 Aligned_cols=287 Identities=14% Similarity=0.135 Sum_probs=172.9
Q ss_pred cccccCcchhhccccCcchhhhccccccc-----cce---ec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCC
Q psy10810 12 VKNHLNDLTIKLRDINPKIICIQESHLKE-----EEN---FT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPR 82 (786)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~---ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r 82 (786)
+.+.++..+.| |||+++|+++..... ..+ .| +|+||+|+|+. |+..|.++.-+.-++.++...|...
T Consensus 328 y~~~fst~shg---fRpglSc~tAi~~~~n~f~gcnw~ie~DLkkcfdtIphd~-LI~eL~~rIkdk~fidL~~kll~AG 403 (796)
T KOG4768|consen 328 YGGEFSTVSHG---FRPGLSCKTAILKTHNLFRGCNWFIEVDLKKCFDTIPHDE-LIIELQKRIKDKGFIDLNYKLLRAG 403 (796)
T ss_pred hcceeeeeecc---cCCCchhhHHHHHHHHHhhccceEEechHHHHhccccHHH-HHHHHHHHHhhhhHHHHHHHHHhcC
Confidence 34556666666 999999999944432 223 36 99999999999 9999999988999999999999876
Q ss_pred eeEEEECCceeecceecccccCCCccccchhHHHHHHhhhhhcccccccccccccchhhccccc-hhHHHHHHhhhc---
Q psy10810 83 SFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKN-KEVLVSIMQESI--- 158 (786)
Q Consensus 83 ~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~~~~d~~~~~~~~~-~~~~~~~l~~~~--- 158 (786)
+.....+- ..-.-|.|||+|+||+|+|+|+..|+.++..-....+ -+|.-+. +...++.|-+.+
T Consensus 404 y~ten~ry------~~~~lGtpqgsvvspil~nifL~~LDk~Lenk~~nef------n~~~~~~~rhs~yr~L~~~iaka 471 (796)
T KOG4768|consen 404 YTTENARY------HVEFLGTPQGSVVSPILCNIFLRELDKRLENKHRNEF------NAGHLRSARHSKYRNLSDSIAKA 471 (796)
T ss_pred ccccccce------ecccccccccccCCchhHHHHHHHHHHHHHHHHHhhh------cccCcccccChhhhhHHHHHHHH
Confidence 66543221 1223499999999999999999999988855221110 0111111 111111121111
Q ss_pred ---cccccceeeecCcCCCCcchHHHHHHHhhccccccCCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhh
Q psy10810 159 ---DTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSND 235 (786)
Q Consensus 159 ---~~~s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~ 235 (786)
...+.......|++---+..|- . ......+.||||+++.+.++- ....+.+..+..++.+
T Consensus 472 Kl~s~~sKtirlrd~~qrn~~n~~~-------g-----fkr~~yVRyadd~ii~v~GS~-----nd~K~ilr~In~f~ss 534 (796)
T KOG4768|consen 472 KLTSGMSKTIRLRDGVQRNETNDTA-------G-----FKRLMYVRYADDIIIGVWGSV-----NDCKQILRDINNFLSS 534 (796)
T ss_pred HHhhhhhhhhhhhhcccccccCCcc-------c-----cceeeEEEecCCEEEEEeccH-----HHHHHHHHHHHHHHHh
Confidence 1222333333333322211110 0 234568999999999999864 3467788888888999
Q ss_pred cCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecc----eEE---eeeEecCC--CchHHHHHHHHHHHHhhhHH
Q psy10810 236 TGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDT----FKF---LGLTFDKK--MTWKVHLKNLKQSCLSRSRI 306 (786)
Q Consensus 236 ~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~----~ky---LGv~id~~--l~~~~hi~~~~~ka~~~~~~ 306 (786)
.||++|++||++.+-.... ... |..|...+- ... -|+-+.+. ...+.-++.+..|.+..-..
T Consensus 535 lGls~n~~kt~it~S~eg~-------~fl--g~nis~tP~r~~~~~~~gh~~i~~rn~~~i~inAPir~I~~KLr~~G~~ 605 (796)
T KOG4768|consen 535 LGLSNNSSKTQITVSREGT-------HFL--GYNISTTPGRPAAGEGGGHWAIRIRNETPIKINAPIRKILRKLRDRGYC 605 (796)
T ss_pred hCcccCcccceEEeeccce-------eee--eceeccCCCCccceeccccceEEeccCCceeecchHHHHHHHHHhccee
Confidence 9999999999987643321 111 222222111 111 11111111 22344555555555443322
Q ss_pred HHHhh-----ccccccCHHHHHHHHHHHhhccccccccc
Q psy10810 307 LKILS-----KKAWAADRKMLIRIYKSLIRSKLDYGCPV 340 (786)
Q Consensus 307 l~~l~-----~~~~g~~~~~~~~ly~a~v~p~l~Yg~~v 340 (786)
..... ...-..+.+++...|.++.++.+.|..-+
T Consensus 606 s~~r~~Pr~V~rlt~~e~rtIin~~~ai~rg~lnYYr~a 644 (796)
T KOG4768|consen 606 SHGRPWPRHVGRLTNEEDRTIINWYAAIGRGILNYYRLA 644 (796)
T ss_pred ecCCcCceeeeeecccCHHHHHHHHHHHhhchhhhhhHh
Confidence 22111 00113578999999999999999998643
No 16
>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=99.53 E-value=9.6e-15 Score=133.81 Aligned_cols=104 Identities=20% Similarity=0.252 Sum_probs=82.6
Q ss_pred cccccceeeecCcCCCCcchHHHHHHHhhcccccc-------CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHH
Q psy10810 159 DTLSEDFSIVCGIPQGGVVSGTLFAIAINSITSYI-------HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLEN 231 (786)
Q Consensus 159 ~~~s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~-------~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~ 231 (786)
|.++..+..++|+|||+++||+||+++++.+.+.+ ......++||||+++++.+. ..+++.++.+..
T Consensus 8 ~~~~~~~~~~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~------~~~~~~~~~l~~ 81 (119)
T cd01648 8 DSIPQYYRQKVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSL------DKAIKFLNLLLR 81 (119)
T ss_pred cchhhhhhhcCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCH------HHHHHHHHHHHH
Confidence 45556778889999999999999999999888765 23567899999999988763 347889999999
Q ss_pred HH-hhcCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEeeeEec
Q psy10810 232 FS-NDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTFD 284 (786)
Q Consensus 232 w~-~~~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~id 284 (786)
+. ++.||++|++||++...... ....+.+.|||+.|+
T Consensus 82 ~l~~~~gl~iN~~Kt~~~~~~~~----------------~~~~~~~~flG~~i~ 119 (119)
T cd01648 82 GFINQYKTFVNFDKTQINFSFAQ----------------LDSSDLIPWCGLLIN 119 (119)
T ss_pred hhHHhhCeEECcccceeeccccc----------------cCCCCccCceeEeeC
Confidence 97 99999999999998653210 123356889999875
No 17
>PRK07708 hypothetical protein; Validated
Probab=99.52 E-value=1.4e-13 Score=138.50 Aligned_cols=128 Identities=20% Similarity=0.204 Sum_probs=97.8
Q ss_pred CCCcEEEEecCCC--CCCCeeEEEEeC--CCcce----EEecCCCCcccHHHHHHHHHHHHHHHHHcCCCc--EEEEeCc
Q psy10810 512 FQSHIKIYTDGSK--NEQGVGCALTIP--EKNIA----KRFGLNKNASIFHAELFALLQSLLTIKELGACK--ALIITDS 581 (786)
Q Consensus 512 ~~~~~~iytDGS~--~~~~~G~a~~~~--~~~~~----~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~--i~I~sDs 581 (786)
.++.+.+|+|||. .++++|+|+++. .+... ....++..++++.||+.|++.||+.+.+.+.+. |.|++||
T Consensus 70 ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DS 149 (219)
T PRK07708 70 EPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDS 149 (219)
T ss_pred CCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEecc
Confidence 4667999999998 355688888773 23222 123455568999999999999999999987654 8999999
Q ss_pred HHHHHHHhc-cCCCcH----HHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhcCCCCC
Q psy10810 582 LSCLQAITN-MFHENP----LVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINNDVTH 643 (786)
Q Consensus 582 ~~a~~~l~~-~~~~~~----~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~~~~~ 643 (786)
+.+++.+++ |....+ +...+...+.+....+.+.||| +..|+.||+||++|+.....+
T Consensus 150 qlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~~ 212 (219)
T PRK07708 150 QVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVIE 212 (219)
T ss_pred HHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCCC
Confidence 999999988 544443 4455555666655668889998 778999999999999866544
No 18
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.26 E-value=5.2e-11 Score=131.74 Aligned_cols=121 Identities=23% Similarity=0.320 Sum_probs=92.7
Q ss_pred cEEEEecCCCC-C-CCeeEEEEeCC--Cc-c-eEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHH
Q psy10810 515 HIKIYTDGSKN-E-QGVGCALTIPE--KN-I-AKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAI 588 (786)
Q Consensus 515 ~~~iytDGS~~-~-~~~G~a~~~~~--~~-~-~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l 588 (786)
.+.||||||+. + +.+|+|+++.+ +. . .........++++.||+.|++.||+.+.+.+...+.|++||+.+++.+
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i 81 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM 81 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence 37899999993 3 45888888732 22 2 233333347899999999999999999998889999999999999999
Q ss_pred hc-cCCCc----HHHHHHHHHHhcCCCcEEEEEecCCCCCCcchHHhHHHHHHhcCC
Q psy10810 589 TN-MFHEN----PLVKRVQEELSSIEPSIEFLWCPSHVGIAGNEAADEEAKQAINND 640 (786)
Q Consensus 589 ~~-~~~~~----~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne~AD~lAk~a~~~~ 640 (786)
.+ |.... .++.++..++++. ..+.+.||| ..+|+.||.||++|....
T Consensus 82 ~~~~~~~~~~l~~~~~~i~~l~~~f-~~~~i~~v~----r~~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 82 SGRWKVKHPDMKPLAAQARELASQF-GRVTYTWIP----RARNAHADRLANEAMDAA 133 (372)
T ss_pred CCCCccCChHHHHHHHHHHHHHhcC-CceEEEECC----chhhhHHHHHHHHHHHhh
Confidence 87 43232 3445566665543 679999999 478999999999997554
No 19
>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=99.17 E-value=5.9e-11 Score=104.94 Aligned_cols=71 Identities=24% Similarity=0.376 Sum_probs=63.9
Q ss_pred cCCCCcchHHHHHHHhhcccccc---CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCeeE
Q psy10810 171 IPQGGVVSGTLFAIAINSITSYI---HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQC 247 (786)
Q Consensus 171 vpQGs~LSPlLF~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT~~ 247 (786)
+|||+++||+||+++++.+...+ ..++....|+||+++.+.+. .++..+..+..+++++|+.+|++||+.
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~-------~~~~~~~~l~~~l~~~gl~ln~~Kt~~ 84 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE-------QQAVKKRELEEFLARLGLNLSDEKTQF 84 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH-------HHHHHHHHHHHHHHHcCcEEChheeEE
Confidence 99999999999999999998876 46788999999999997765 478889999999999999999999987
Q ss_pred E
Q psy10810 248 V 248 (786)
Q Consensus 248 ~ 248 (786)
.
T Consensus 85 ~ 85 (98)
T cd00304 85 T 85 (98)
T ss_pred e
Confidence 4
No 20
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.94 E-value=4.9e-09 Score=90.22 Aligned_cols=82 Identities=29% Similarity=0.327 Sum_probs=67.6
Q ss_pred cHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhccCCC----cHHHHHHHHHHhcCCCcEEEEEecCCCCCCcch
Q psy10810 552 IFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNMFHE----NPLVKRVQEELSSIEPSIEFLWCPSHVGIAGNE 627 (786)
Q Consensus 552 ~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~~~~----~~~~~~i~~~~~~~~~~v~~~wvpgH~g~~~Ne 627 (786)
+..||+.|+..||+.+.+.+..++.|.|||+.+++.+++.... ..++++|...++. -..+.+.||| .++|.
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~----r~~N~ 75 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIP----REQNK 75 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE------GGGSH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEC----hHHhH
Confidence 4689999999999999999999999999999999999885322 3577888888876 5789999999 99999
Q ss_pred HHhHHHHHHhc
Q psy10810 628 AADEEAKQAIN 638 (786)
Q Consensus 628 ~AD~lAk~a~~ 638 (786)
.||.|||.|.+
T Consensus 76 ~A~~LA~~a~~ 86 (87)
T PF13456_consen 76 VADALAKFALS 86 (87)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhh
Confidence 99999999874
No 21
>KOG1005|consensus
Probab=98.79 E-value=2.1e-08 Score=114.05 Aligned_cols=122 Identities=18% Similarity=0.213 Sum_probs=85.8
Q ss_pred HHHhhhcccccccee-eecCcCCCCcchHHHHHHHhhcccccc------CCCCceeeeecceeEEeccCChHHHHHHHHH
Q psy10810 152 SIMQESIDTLSEDFS-IVCGIPQGGVVSGTLFAIAINSITSYI------HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQE 224 (786)
Q Consensus 152 ~~l~~~~~~~s~~~~-~~~GvpQGs~LSPlLF~l~~~~l~~~~------~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~ 224 (786)
..|-.+.-++.+..+ ...|+||||+||-+|..+|++++.+.. +..+..+.|+||..+++... +++.+
T Consensus 615 ~~l~~~~vki~~k~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt~~------~~a~k 688 (888)
T KOG1005|consen 615 NMLSTNYVKIGGKSYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITTEN------DQAKK 688 (888)
T ss_pred HHHhhheEEECCeEEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEecCH------HHHHH
Confidence 333344444555444 457999999999999999999999875 33357999999999998864 44788
Q ss_pred HHHHHHHHHhhcCCccCCCCeeEEEecccCcCCCcceeeecCCceeeeecceEEeeeEecCC
Q psy10810 225 SIDKLENFSNDTGLFFSPQKSQCVLFSRKYKQLNTSINLNMYDTRIEVVDTFKFLGLTFDKK 286 (786)
Q Consensus 225 ~l~~l~~w~~~~gL~ln~~KT~~~~f~~~~~~~~~~~~~~~~g~~I~~~~~~kyLGv~id~~ 286 (786)
.+..+..=..+++...|.+||. .|..+.........+.++. ..-+.|=|+.+++.
T Consensus 689 fl~~l~~Gf~~yn~~tn~~K~~--nF~~se~~~~~~~f~~~~~-----~~~f~w~g~~i~st 743 (888)
T KOG1005|consen 689 FLKLLSRGFNKYNFFTNEPKTV--NFEVSEECGASIVFVWMHK-----HLLFQWCGLLIRST 743 (888)
T ss_pred HHHHHhccccccceeccCcccc--cccchhccCcceeeeccCc-----cccccccceeeecc
Confidence 8888888888899999999987 6665554432222222111 14466777777763
No 22
>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=98.50 E-value=2.4e-07 Score=84.95 Aligned_cols=72 Identities=14% Similarity=0.259 Sum_probs=56.1
Q ss_pred CcCCCCcchHHHHHHHhhcccccc-CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHH-HHhhcCCccCCCCeeE
Q psy10810 170 GIPQGGVVSGTLFAIAINSITSYI-HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLEN-FSNDTGLFFSPQKSQC 247 (786)
Q Consensus 170 GvpQGs~LSPlLF~l~~~~l~~~~-~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~-w~~~~gL~ln~~KT~~ 247 (786)
=+|||-..||.+|.-+++.+...+ ..+..+..|+||+.|.+.+. +. .++.+..+.+ .++++|+.+|++||++
T Consensus 33 ~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~~---~~---~~~~~~~l~~~~l~~~gl~ln~~K~~~ 106 (119)
T cd03714 33 ALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASSI---KT---SEAVLRHLRATLLANLGFTLNLEKSKL 106 (119)
T ss_pred ecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCcH---HH---HHHHHHHHHHHHHHHcCCccChhhcEe
Confidence 389999999999999999988765 34567899999999987752 22 3444444443 6889999999999985
No 23
>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=98.37 E-value=3.4e-07 Score=93.10 Aligned_cols=72 Identities=22% Similarity=0.233 Sum_probs=60.6
Q ss_pred cCcCCCCcchHHHHHHHhhcccccc---CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCe
Q psy10810 169 CGIPQGGVVSGTLFAIAINSITSYI---HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKS 245 (786)
Q Consensus 169 ~GvpQGs~LSPlLF~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT 245 (786)
..+|||...||.+|+.+++.++..+ ........|+||++|.+.+. +...+.++.+...++++|+.+|++||
T Consensus 127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~------~~~~~~l~~v~~~l~~~gl~ln~~K~ 200 (213)
T cd01645 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE------GQLREIYEELRQTLLRWGLTIPPEKV 200 (213)
T ss_pred EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCH------HHHHHHHHHHHHHHHHCCCEeCHHHE
Confidence 5799999999999999999998765 23556889999999986643 33677888888888999999999999
Q ss_pred e
Q psy10810 246 Q 246 (786)
Q Consensus 246 ~ 246 (786)
+
T Consensus 201 ~ 201 (213)
T cd01645 201 Q 201 (213)
T ss_pred e
Confidence 7
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=98.15 E-value=8.5e-07 Score=81.23 Aligned_cols=47 Identities=26% Similarity=0.321 Sum_probs=38.8
Q ss_pred ccccCCCccccchhHHHHHHhhhhhcccc-------cccccccccchhhccccc
Q psy10810 100 VCGIPQGGVVSGTLFAIAINSITSYIHPS-------LSSSLFVDDFAIFTRDKN 146 (786)
Q Consensus 100 ~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~-------~~~~~~~~d~~~~~~~~~ 146 (786)
..|+|||+++||+||+++++.++..+... ....-||||..+++++..
T Consensus 17 ~~GlpQG~~lSp~L~nl~l~~l~~~~~~~~~~~~~~~~~~rYaDD~li~~~~~~ 70 (119)
T cd01648 17 KVGIPQGSPLSSLLCSLYYADLENKYLSFLDVIDKDSLLLRLVDDFLLITTSLD 70 (119)
T ss_pred cCcccCCcchHHHHHHHHHHHHHHHHHhhcccCCCCceEEEEeCcEEEEeCCHH
Confidence 46999999999999999999999987542 345668999988887744
No 25
>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=97.96 E-value=7.1e-06 Score=83.29 Aligned_cols=74 Identities=26% Similarity=0.262 Sum_probs=60.8
Q ss_pred ecCcCCCCcchHHHHHHHhhcccccc---CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCC
Q psy10810 168 VCGIPQGGVVSGTLFAIAINSITSYI---HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQK 244 (786)
Q Consensus 168 ~~GvpQGs~LSPlLF~l~~~~l~~~~---~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~K 244 (786)
-.-+|||-..||.+|.-+++.++..+ ..+.....|.||+.|...+ . +...+.++.+...++++|+.+|++|
T Consensus 122 ~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~~~~~~~~~Y~DDili~s~~--~----~e~~~~l~~v~~~l~~~gl~l~~~K 195 (210)
T cd03715 122 FTRLPQGFKNSPTLFHEALARDLAPFPLEHEGTILLQYVDDLLLAADS--E----EDCLKGTDALLTHLGELGYKVSPKK 195 (210)
T ss_pred EEEEeccccCcHHHHHHHHHHHHHHHHhhCCCeEEEEECCcEEEecCC--H----HHHHHHHHHHHHHHHHCCCCcCHHH
Confidence 35789999999999999999887765 2456788999999998654 2 3367778888888899999999999
Q ss_pred eeE
Q psy10810 245 SQC 247 (786)
Q Consensus 245 T~~ 247 (786)
|+.
T Consensus 196 ~~~ 198 (210)
T cd03715 196 AQI 198 (210)
T ss_pred eeC
Confidence 974
No 26
>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=97.45 E-value=8.3e-05 Score=75.72 Aligned_cols=56 Identities=20% Similarity=0.370 Sum_probs=45.6
Q ss_pred cCCCccccchhHHHHHHhhhhhcc-----cccccccccccchhhccccc---hhHHHHHHhhhc
Q psy10810 103 IPQGGVVSGTLFAIAINSITSYIH-----PSLSSSLFVDDFAIFTRDKN---KEVLVSIMQESI 158 (786)
Q Consensus 103 v~qg~~~sp~l~~~~~n~l~~~~~-----~~~~~~~~~~d~~~~~~~~~---~~~~~~~l~~~~ 158 (786)
||||+++||+|++++++.++..+. ......-||||..++|.+.. ...+...+++.+
T Consensus 104 lpQG~~lSp~Lanl~l~~~d~~l~~~~~~~~~~~~RYaDD~~i~~~~~~~~~~~~~~~~i~~~l 167 (214)
T cd03487 104 LPQGAPTSPALSNLVFRKLDERLSKLAKSNGLTYTRYADDITFSSNKKLKEALDKLLEIIRSIL 167 (214)
T ss_pred cCCCCcccHHHHHHHHHHHHHHHHHHHHHcCCeEEEEeccEEEEccccchhHHHHHHHHHHHHH
Confidence 799999999999999999999884 34567889999999998875 555666666544
No 27
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=97.08 E-value=0.00048 Score=73.07 Aligned_cols=58 Identities=14% Similarity=0.175 Sum_probs=47.0
Q ss_pred cccCCCccccchhHHHHHHhhhhhccccccccc---ccccchhhccccchhHHHHHHhhhc
Q psy10810 101 CGIPQGGVVSGTLFAIAINSITSYIHPSLSSSL---FVDDFAIFTRDKNKEVLVSIMQESI 158 (786)
Q Consensus 101 ~Gv~qg~~~sp~l~~~~~n~l~~~~~~~~~~~~---~~~d~~~~~~~~~~~~~~~~l~~~~ 158 (786)
+|+|||+++||+|-|+|++.|+...+....+.. |+||..++++...-......|++.+
T Consensus 82 rGtPqGgviSplLaNiyL~~lD~~v~~~~~g~~l~RYaDD~vi~~~~~~a~~aw~~i~~fl 142 (346)
T cd01709 82 RGTPMSHALSDVFGELVLFCLDFAVNQATDGGLLYRLHDDLWFWGQPETCAKAWKAIQEFA 142 (346)
T ss_pred CccCCCchhhHHHHHHHHHHHHHHHHhcCCCceEEEEcCeEEEEcCHHHHHHHHHHHHHHH
Confidence 699999999999999999999999987544433 4999999977666666667777754
No 28
>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=97.01 E-value=0.00085 Score=65.31 Aligned_cols=72 Identities=18% Similarity=0.305 Sum_probs=55.8
Q ss_pred cCcCCCCcchHHHHHHHhhccccccCCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCeeE
Q psy10810 169 CGIPQGGVVSGTLFAIAINSITSYIHPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQC 247 (786)
Q Consensus 169 ~GvpQGs~LSPlLF~l~~~~l~~~~~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT~~ 247 (786)
..+|||...||.+|.-.+..++..+ .......|+||+.+.... .++ ....++.+..-.+++|+.+|++||+.
T Consensus 94 ~~~p~G~~~s~~~~~~~~~~~l~~~-~~~~~~~y~DDi~i~~~~--~~~----~~~~~~~~~~~l~~~~~~~~~~K~~~ 165 (177)
T cd01647 94 TRMPFGLKNAPATFQRLMNKILGDL-LGDFVEVYLDDILVYSKT--EEE----HLEHLREVLERLREAGLKLNPEKCEF 165 (177)
T ss_pred EEecCCCccHHHHHHHHHHhhhccc-cccccEEEecCccccCCC--HHH----HHHHHHHHHHHHHHcCCEeCHHHcee
Confidence 5699999999999999999888764 234577899999998664 322 44555566666678999999999974
No 29
>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=97.00 E-value=0.0004 Score=71.10 Aligned_cols=56 Identities=30% Similarity=0.524 Sum_probs=44.0
Q ss_pred cccCCCccccchhHHHHHHhhhhhccc--------------ccccccccccchhhccccc-hhHHHHHHhh
Q psy10810 101 CGIPQGGVVSGTLFAIAINSITSYIHP--------------SLSSSLFVDDFAIFTRDKN-KEVLVSIMQE 156 (786)
Q Consensus 101 ~Gv~qg~~~sp~l~~~~~n~l~~~~~~--------------~~~~~~~~~d~~~~~~~~~-~~~~~~~l~~ 156 (786)
.|||||+++||+||+++++.++..+.. ......|+||..+++++.+ ...+...++.
T Consensus 125 ~GlpqG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~~~~~~~rY~DD~~i~~~~~~~~~~~~~~i~~ 195 (226)
T cd01651 125 KGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKFRRLRYVRYADDFVIGVRGPKEAEEIKELIRE 195 (226)
T ss_pred CCcCCCccHHHHHHHHHHHHHHHHHHHhhhhcccccccccCceEEEEecCceEEecCCHHHHHHHHHHHHH
Confidence 599999999999999999999999864 3456778999999988866 3333333433
No 30
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=96.80 E-value=0.001 Score=72.46 Aligned_cols=106 Identities=19% Similarity=0.148 Sum_probs=73.9
Q ss_pred cccccCcchhhccccCcchhhhccccc-------ccc----ce--ec-ccccccccchHHHHHHHHhccCCCChHHHHHh
Q psy10810 12 VKNHLNDLTIKLRDINPKIICIQESHL-------KEE----EN--FT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSK 77 (786)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~----~~--ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~ 77 (786)
+...+++..|| |+|+.+|+++... ... .+ .| .++||+++|.. ++..+...--+...+.++.-
T Consensus 144 ~~~~f~~~s~G---f~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~di~~~fd~~~h~~-ll~~~~~~i~~~~~~~~~~r 219 (328)
T COG3344 144 IENIFSPLSYG---FRPGPSASNAIAYAFDLPQGKICSPNGWVYDRDIKKCFDSINHKL-LLYALDVTISDKLVLLLLGR 219 (328)
T ss_pred HHhccccCCCC---CCCChhHHHHHHHHHhhhccCCCCCceEEEeehHHHHhcccCHHH-HHHHhHhhhcchHHHHHHHH
Confidence 66778999999 9999999988211 112 33 45 99999999999 99999888334433434433
Q ss_pred hhCCCeeEEEECCceeecceecccccCCCccccchhHHHHHHhhhhhccc
Q psy10810 78 YMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIHP 127 (786)
Q Consensus 78 ~l~~r~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~~ 127 (786)
.+....... .+ ....-..|+|||+++||+|.|+.++.+...+..
T Consensus 220 ~~~~~~~~~--~~----~~~~~~~~~~q~~~vs~~l~n~~l~~~~~~~~~ 263 (328)
T COG3344 220 ILIAGYKTK--FN----LKKSKEKGTPQGGLVSPILVNIKLSKLDNELRN 263 (328)
T ss_pred HHHccccee--ec----ccccccccCCCCCccCchhhhhhhhhhhHHHHH
Confidence 333332222 11 122335699999999999999999988766655
No 31
>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=96.77 E-value=0.0007 Score=65.39 Aligned_cols=59 Identities=24% Similarity=0.422 Sum_probs=45.4
Q ss_pred ccccCCCccccchhHHHHHHhhhhhccc---ccccccccccchhhccccchh-HHHHHHhhhc
Q psy10810 100 VCGIPQGGVVSGTLFAIAINSITSYIHP---SLSSSLFVDDFAIFTRDKNKE-VLVSIMQESI 158 (786)
Q Consensus 100 ~~Gv~qg~~~sp~l~~~~~n~l~~~~~~---~~~~~~~~~d~~~~~~~~~~~-~~~~~l~~~~ 158 (786)
..|+|||+++||+|++++++.++..+.. .....-||||..+++++.... .....+.+.+
T Consensus 51 ~~GlpqG~~lS~~L~~~~l~~~d~~i~~~~~~~~~~RY~DD~~i~~~~~~~~~~~~~~i~~~l 113 (158)
T cd01646 51 TNGLPIGPLTSRFLANIYLNDVDHELKSKLKGVDYVRYVDDIRIFADSKEEAEEILEELKEFL 113 (158)
T ss_pred CceEccCcchHHHHHHHHHHHHHHHHHhccCCceEEEecCcEEEEcCCHHHHHHHHHHHHHHH
Confidence 3599999999999999999999999964 566677899999998774432 3344444433
No 32
>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=95.99 E-value=0.005 Score=53.93 Aligned_cols=43 Identities=21% Similarity=0.428 Sum_probs=38.1
Q ss_pred cCCCccccchhHHHHHHhhhhhcc---cccccccccccchhhcccc
Q psy10810 103 IPQGGVVSGTLFAIAINSITSYIH---PSLSSSLFVDDFAIFTRDK 145 (786)
Q Consensus 103 v~qg~~~sp~l~~~~~n~l~~~~~---~~~~~~~~~~d~~~~~~~~ 145 (786)
+|||+++||.||+++++.+...+. .......|+||..+++++.
T Consensus 12 lPqG~~~Sp~l~~~~~~~l~~~~~~~~~~~~~~~Y~DD~~i~~~~~ 57 (98)
T cd00304 12 LPQGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSE 57 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHHHHHhcCCceEEEeeCcEEEEeCcH
Confidence 899999999999999999999874 4566788999999998876
No 33
>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=95.90 E-value=0.004 Score=62.80 Aligned_cols=47 Identities=28% Similarity=0.504 Sum_probs=40.1
Q ss_pred ccccCCCccccchhHHHHHHhhhhhcccc----cccccccccchhhccccc
Q psy10810 100 VCGIPQGGVVSGTLFAIAINSITSYIHPS----LSSSLFVDDFAIFTRDKN 146 (786)
Q Consensus 100 ~~Gv~qg~~~sp~l~~~~~n~l~~~~~~~----~~~~~~~~d~~~~~~~~~ 146 (786)
..|+|||+++||+||+++++.+...+... .....|+||..+++.+..
T Consensus 123 ~~glpqG~~~S~~l~~~~l~~l~~~~~~~~~~~~~~~rY~DD~~i~~~~~~ 173 (214)
T PF00078_consen 123 KRGLPQGSPLSPLLFNIYLDDLDRELQQELNPDISYLRYADDILIISKSKE 173 (214)
T ss_dssp ESBS-TTSTCHHHHHHHHHHHHHHHHHHHS-TTSEEEEETTEEEEEESSHH
T ss_pred cccccccccccchhhccccccccccccccccccccceEeccccEEEECCHH
Confidence 35999999999999999999999999774 467889999999988833
No 34
>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=95.62 E-value=0.039 Score=58.48 Aligned_cols=76 Identities=12% Similarity=0.223 Sum_probs=49.9
Q ss_pred eeeecCcCCCCcch----HHHHHHHhhcccccc-----CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhh
Q psy10810 165 FSIVCGIPQGGVVS----GTLFAIAINSITSYI-----HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSND 235 (786)
Q Consensus 165 ~~~~~GvpQGs~LS----PlLF~l~~~~l~~~~-----~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~ 235 (786)
+....|.|+|++.. +++-++++......+ ...+....|.||.++.+.... .....+.+.+++++
T Consensus 154 ~~~~~G~pSG~~~T~~~Nsl~n~~~~~~a~~~~~~~~~~~~~~~~~~GDD~li~~~~~~-------~~~~~~~~~~~~~~ 226 (278)
T cd01699 154 YKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVRLLNYGDDCLLSVEKAD-------DKFNLETLAEWLKE 226 (278)
T ss_pred EEEcCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhceEEEEEcCCeEEEechhH-------hhhCHHHHHHHHHH
Confidence 34457888888764 333344433333222 256778999999999877531 12344567778888
Q ss_pred cCCccCCCCeeE
Q psy10810 236 TGLFFSPQKSQC 247 (786)
Q Consensus 236 ~gL~ln~~KT~~ 247 (786)
.|++++++|...
T Consensus 227 ~G~~~~~~~~~~ 238 (278)
T cd01699 227 YGLTMTDEDKVE 238 (278)
T ss_pred cCCEeCCcccCC
Confidence 999999999865
No 35
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=94.41 E-value=0.021 Score=48.85 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=25.5
Q ss_pred ccccCCCCCCCCCCCCC-ccCccccccccccc
Q psy10810 718 SHLFRREDQPICDQCQE-PMTIEHILISCRKM 748 (786)
Q Consensus 718 ~~~~~~~~~~~C~~Cg~-~~t~~H~l~~Cp~~ 748 (786)
+++.+...++.|+.|+. +||.+|+|++||..
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCc
Confidence 34556677899999995 89999999999964
No 36
>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=94.26 E-value=0.034 Score=56.53 Aligned_cols=45 Identities=16% Similarity=0.292 Sum_probs=29.0
Q ss_pred ccCCCccccchhHHHHHHhhhhh-----cccccccccccccchhhccccc
Q psy10810 102 GIPQGGVVSGTLFAIAINSITSY-----IHPSLSSSLFVDDFAIFTRDKN 146 (786)
Q Consensus 102 Gv~qg~~~sp~l~~~~~n~l~~~-----~~~~~~~~~~~~d~~~~~~~~~ 146 (786)
|.+-+..++=+..+-..+.+... .........|+||..+++.+..
T Consensus 110 G~~lSp~l~~l~~~~l~~~~~~~~~~~~~~~~~~~~~yaDD~~i~~~~~~ 159 (220)
T cd01650 110 GDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKS 159 (220)
T ss_pred CCcccHHHHHHHHHHHHHHHHhhccccCCCCccceEEeccceeeeccCCH
Confidence 44444455555555666666543 2445667889999999988875
No 37
>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=93.55 E-value=0.057 Score=54.76 Aligned_cols=68 Identities=15% Similarity=0.172 Sum_probs=52.7
Q ss_pred ecCcCCCCcchHHHHHHHhhccccccCC-----CCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccC
Q psy10810 168 VCGIPQGGVVSGTLFAIAINSITSYIHP-----SLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFS 241 (786)
Q Consensus 168 ~~GvpQGs~LSPlLF~l~~~~l~~~~~~-----~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln 241 (786)
-.-+|+|-.-||.+|..+++.+...+.. .+....|.||+.+.+.+ . ..++..++.+.+.+++.|+.+.
T Consensus 101 ~~~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s--~----~e~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 101 MTVVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDT--L----NEAVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred EEEEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCC--H----HHHHHHHHHHHHHHHhCCccch
Confidence 3559999999999999999999987633 23467999999997664 2 3466777777777788998773
No 38
>KOG4768|consensus
Probab=88.65 E-value=0.29 Score=55.17 Aligned_cols=30 Identities=30% Similarity=0.378 Sum_probs=25.1
Q ss_pred ceeeecCcCCCCcchHHHHHHHhhcccccc
Q psy10810 164 DFSIVCGIPQGGVVSGTLFAIAINSITSYI 193 (786)
Q Consensus 164 ~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~ 193 (786)
...-.-|+||||+.||+|.|+|+..|.+.+
T Consensus 411 y~~~~lGtpqgsvvspil~nifL~~LDk~L 440 (796)
T KOG4768|consen 411 YHVEFLGTPQGSVVSPILCNIFLRELDKRL 440 (796)
T ss_pred eecccccccccccCCchhHHHHHHHHHHHH
Confidence 344456999999999999999999987765
No 39
>KOG1005|consensus
Probab=75.76 E-value=2.7 Score=49.67 Aligned_cols=69 Identities=19% Similarity=0.356 Sum_probs=45.9
Q ss_pred ChHHHHHhhhCCCeeEEEECCceeecceecccccCCCccccchhHHHHHHhhhhhcc-cccccc-----cccccchhhcc
Q psy10810 70 HLPIFLSKYMDPRSFKIRLNNSILSENFSIVCGIPQGGVVSGTLFAIAINSITSYIH-PSLSSS-----LFVDDFAIFTR 143 (786)
Q Consensus 70 ~~~~~i~~~l~~r~~~v~~~~~~~s~~~~~~~Gv~qg~~~sp~l~~~~~n~l~~~~~-~~~~~~-----~~~~d~~~~~~ 143 (786)
.+..||.+++++-. |+++|. ......|+|||+++|-+|+.+|.++|.+..- ...+.+ =||||.-+.+.
T Consensus 608 ~l~~vi~~~l~~~~--vki~~k----~yvq~~GIpQGs~LSslLc~lyy~dle~~y~~~~~~~g~~vLlR~vDDFLfITt 681 (888)
T KOG1005|consen 608 DLFSVIRNMLSTNY--VKIGGK----SYVQKKGIPQGSILSSLLCHLYYGDLEDKYFSFEKEDGSIVLLRYVDDFLFITT 681 (888)
T ss_pred hHHHHHHHHHhhhe--EEECCe----EEEEecCccCCCchhHHHHHHHHHhHHHHHhhcccCCCcEEEEEeecceEEEec
Confidence 35667777776543 455652 2344569999999999999999999987662 222222 35888655544
Q ss_pred c
Q psy10810 144 D 144 (786)
Q Consensus 144 ~ 144 (786)
+
T Consensus 682 ~ 682 (888)
T KOG1005|consen 682 E 682 (888)
T ss_pred C
Confidence 4
No 40
>PF09004 DUF1891: Domain of unknown function (DUF1891); InterPro: IPR015095 This domain is found at the extreme N terminus of eukaryotic alkylated DNA repair protein homologs. ; GO: 0008168 methyltransferase activity, 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 2CQ2_A 3THT_C 3THP_A.
Probab=69.66 E-value=0.71 Score=33.32 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=6.7
Q ss_pred hHHHHHHHHHHHHhhhHHHHHhhccccccCHHHHHHHHHHHhh
Q psy10810 289 WKVHLKNLKQSCLSRSRILKILSKKAWAADRKMLIRIYKSLIR 331 (786)
Q Consensus 289 ~~~hi~~~~~ka~~~~~~l~~l~~~~~g~~~~~~~~ly~a~v~ 331 (786)
|+.|+..+.+|+..++..||.+.+. .++...+..+|+++|.
T Consensus 1 W~~n~~~~~KKa~qRlyFLRkl~k~--~~~~~~l~lfY~s~Ie 41 (42)
T PF09004_consen 1 WTSNTTSLYKKAQQRLYFLRKLRKF--NVDSKLLTLFYHSVIE 41 (42)
T ss_dssp ---------------------------SS-----SHTTTTT--
T ss_pred CCcchHHHHHHHHhHHHHHHHHHHc--cchhHHHHHHHHHHhc
Confidence 6788899999999999999998865 5777777778877764
No 41
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=65.86 E-value=22 Score=34.07 Aligned_cols=55 Identities=18% Similarity=0.300 Sum_probs=34.4
Q ss_pred CCcEEEEecCCCCCCCeeEEEEe---CCCcceEE-----ecC--CCCcccHHHHHHHHHHHHHHHHH
Q psy10810 513 QSHIKIYTDGSKNEQGVGCALTI---PEKNIAKR-----FGL--NKNASIFHAELFALLQSLLTIKE 569 (786)
Q Consensus 513 ~~~~~iytDGS~~~~~~G~a~~~---~~~~~~~~-----~~~--~~~~s~~~aEl~Ai~~aL~~~~~ 569 (786)
...+.+|+|+|. .+.|+.++. .++..... .+. ....|+=+-||.|+..|.+.+..
T Consensus 79 ~~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 79 SVELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred ceeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 346899999994 344544443 12221111 111 13459999999999999988754
No 42
>COG3344 Retron-type reverse transcriptase [DNA replication, recombination, and repair]
Probab=62.34 E-value=13 Score=40.46 Aligned_cols=48 Identities=27% Similarity=0.278 Sum_probs=36.3
Q ss_pred ceeeecCcCCCCcchHHHHHHHhhccccccCC--CCceeeeecceeEEec
Q psy10810 164 DFSIVCGIPQGGVVSGTLFAIAINSITSYIHP--SLSSSLFVDDFAIFTR 211 (786)
Q Consensus 164 ~~~~~~GvpQGs~LSPlLF~l~~~~l~~~~~~--~~~~~~yADD~~i~~~ 211 (786)
......|+|||+++||+|-|+.++.+...+.. ......|+||..+-..
T Consensus 232 ~~~~~~~~~q~~~vs~~l~n~~l~~~~~~~~~~~~~~~~~y~~~~~i~~~ 281 (328)
T COG3344 232 KKSKEKGTPQGGLVSPILVNIKLSKLDNELRNRYLNLLRRYIDDGNIDKL 281 (328)
T ss_pred cccccccCCCCCccCchhhhhhhhhhhHHHHHHHhhhhhhhcccccCCHH
Confidence 33467899999999999999998887765411 1137789999888755
No 43
>CHL00002 matK maturase K
Probab=61.07 E-value=16 Score=41.91 Aligned_cols=54 Identities=13% Similarity=0.119 Sum_probs=39.2
Q ss_pred CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHH-HHHHhhcCCccCCCCeeEEEecc
Q psy10810 194 HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKL-ENFSNDTGLFFSPQKSQCVLFSR 252 (786)
Q Consensus 194 ~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l-~~w~~~~gL~ln~~KT~~~~f~~ 252 (786)
++-++.++||||..|.+.|... . +++.-..+ .=|....++.++|+|+.+-+++.
T Consensus 270 dp~ihYVRYaddfIIg~kGsk~--~---a~KwK~~l~~F~q~~f~l~~s~eKi~I~~ls~ 324 (504)
T CHL00002 270 DPFIHYVRYQGKSILASKGTPL--L---MNKWKYYLVNFWQCHFHLWSQPGRIHINQLSN 324 (504)
T ss_pred cceEEEEEECCcEEEEECCCHH--H---HHHHHHHHHHHHHHhceeeecCCceeeccccC
Confidence 5667899999999999888664 2 34444444 33556789999999998876543
No 44
>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=55.27 E-value=6.2 Score=39.97 Aligned_cols=45 Identities=18% Similarity=0.138 Sum_probs=35.4
Q ss_pred cccCCCccccchhHHHHHHhhhhhcccc---cccccccccchhhcccc
Q psy10810 101 CGIPQGGVVSGTLFAIAINSITSYIHPS---LSSSLFVDDFAIFTRDK 145 (786)
Q Consensus 101 ~Gv~qg~~~sp~l~~~~~n~l~~~~~~~---~~~~~~~~d~~~~~~~~ 145 (786)
.++|||-..||.+|+.+|+.+-..+... ..-..|+||.-+++.+.
T Consensus 127 ~~lP~Gl~~SP~~f~~~m~~~l~~~~~~~~~~~~~~Y~DDili~s~~~ 174 (213)
T cd01645 127 KVLPQGMKNSPTICQSFVAQALEPFRKQYPDIVIYHYMDDILIASDLE 174 (213)
T ss_pred EEeCCCCcChHHHHHHHHHHHHHHHHHHCCCeEEEEEcCCEEEEcCCH
Confidence 4799999999999999999887665432 23357899998887765
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=52.37 E-value=17 Score=35.74 Aligned_cols=90 Identities=20% Similarity=0.287 Sum_probs=52.8
Q ss_pred CCcEEEEecCCCCCCCeeEEEEeCCCcceEEecCCCCcccHHHHHHHHHHHHHHHHHcCCCcEEEEeCcHHHHHHHhccC
Q psy10810 513 QSHIKIYTDGSKNEQGVGCALTIPEKNIAKRFGLNKNASIFHAELFALLQSLLTIKELGACKALIITDSLSCLQAITNMF 592 (786)
Q Consensus 513 ~~~~~iytDGS~~~~~~G~a~~~~~~~~~~~~~~~~~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I~sDs~~a~~~l~~~~ 592 (786)
+.--.||+|+.- +|+|+.+.++.....+.. .-.+..||+.|.-.|.-+. ..++ |.|||..|+. +..
T Consensus 92 ~~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~--~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vls---rky 157 (245)
T PF00336_consen 92 PGLCQVFADATP----TGWGISITGQRMRGTFSK--PLPIHTAELLAACLARLMS----GARC-LGTDNTVVLS---RKY 157 (245)
T ss_pred CCCCceeccCCC----CcceeeecCceeeeeecc--cccchHHHHHHHHHHHhcc----CCcE-EeecCcEEEe---ccc
Confidence 345678898865 455555544544433333 3467899999998776655 3444 9999998772 112
Q ss_pred CC--cHHHHHHHHHHhcCCCcEEEEEecCC
Q psy10810 593 HE--NPLVKRVQEELSSIEPSIEFLWCPSH 620 (786)
Q Consensus 593 ~~--~~~~~~i~~~~~~~~~~v~~~wvpgH 620 (786)
+. |-+.-...-++ ..+.|..||+-
T Consensus 158 ts~PW~lac~A~wiL----rgts~~yVPS~ 183 (245)
T PF00336_consen 158 TSFPWLLACAANWIL----RGTSFYYVPSK 183 (245)
T ss_pred ccCcHHHHHHHHHhh----cCceEEEeccc
Confidence 22 21221222233 36778889943
No 46
>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=40.13 E-value=19 Score=32.49 Aligned_cols=43 Identities=14% Similarity=0.308 Sum_probs=33.8
Q ss_pred ccCCCccccchhHHHHHHhhhhhcccc-cccccccccchhhccc
Q psy10810 102 GIPQGGVVSGTLFAIAINSITSYIHPS-LSSSLFVDDFAIFTRD 144 (786)
Q Consensus 102 Gv~qg~~~sp~l~~~~~n~l~~~~~~~-~~~~~~~~d~~~~~~~ 144 (786)
-+|||-..||.+|..+|+.+-..++.. ..-..|+||.-+++++
T Consensus 33 ~mp~Gl~~sp~~f~~~~~~i~~~~~~~~~~v~~Y~DDili~~~~ 76 (119)
T cd03714 33 ALPFGLSLAPRVFTKVVEALLAPLRLLGVRIFSYLDDLLIIASS 76 (119)
T ss_pred ecCCcccchHHHHHHHHHHHHHHhhcCCeEEEEEecCeEEEeCc
Confidence 479999999999999999888765422 1224689999988876
No 47
>PF03431 RNA_replicase_B: RNA replicase, beta-chain ; InterPro: IPR005093 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This is a family of Leviviridae RNA replicases.; GO: 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3MMP_G 3AVU_A 3AVW_A 3AGQ_A 3AGP_A 3AVT_A 3AVY_A 3AVX_A 3AVV_A.
Probab=40.04 E-value=88 Score=34.98 Aligned_cols=43 Identities=12% Similarity=0.135 Sum_probs=25.1
Q ss_pred cceec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCeeEEEECCce
Q psy10810 41 EENFT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRSFKIRLNNSI 92 (786)
Q Consensus 41 ~~~ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~~~v~~~~~~ 92 (786)
...+| +.|=|+|.... .+.| +|+.+.+.+.++= +-.+.++|..
T Consensus 246 laTIDLSsASDsis~~L--v~~l----lPp~~~~~l~~lR---s~~~~l~g~~ 289 (542)
T PF03431_consen 246 LATIDLSSASDSISLWL--VELL----LPPHWYRYLTDLR---SPYGSLDGKV 289 (542)
T ss_dssp EEEEEBTTCCCT-BHHH--HHHH----S-HHHHHHHHHHS----SEEE-TS-E
T ss_pred ceeEeccccccHhHHHH--HHHh----CCHHHHHHHHHhc---cccceECCEE
Confidence 34589 99999997764 4444 6777777766553 3444467743
No 48
>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=38.01 E-value=1.9e+02 Score=32.91 Aligned_cols=42 Identities=10% Similarity=-0.012 Sum_probs=31.0
Q ss_pred cceec-ccccccccchHHHHHHHHhccCCCChHHHHHhhhCCCee
Q psy10810 41 EENFT-LKGFNTVGTYEVILRQLHKWNMRGHLPIFLSKYMDPRSF 84 (786)
Q Consensus 41 ~~~ld-~~AFD~V~~~~~L~~~L~~~g~~~~~~~~i~~~l~~r~~ 84 (786)
..-|| +.|=|+.+-.. .-+.|... ++..+-.-.++.|.+|.+
T Consensus 150 ~~S~DLsaATDR~Pi~l-Q~~il~~l-~~~~~a~~W~~llv~r~~ 192 (498)
T PF05919_consen 150 FYSFDLSAATDRFPIVL-QERILSYL-FGDSFASSWRSLLVGRPY 192 (498)
T ss_pred eEEEeeccccccccHHH-HHHHHHHH-hCchHHHHHHHHHcCCcc
Confidence 45689 99999999887 66666665 655665566777877766
No 49
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=35.67 E-value=18 Score=27.96 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=10.0
Q ss_pred CCCCCCCCccCcccccccccc
Q psy10810 727 PICDQCQEPMTIEHILISCRK 747 (786)
Q Consensus 727 ~~C~~Cg~~~t~~H~l~~Cp~ 747 (786)
-.|+.||+..+-.|....||+
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 469999999999999999995
No 50
>PHA00028 rep RNA replicase, beta subunit
Probab=33.55 E-value=80 Score=35.79 Aligned_cols=40 Identities=20% Similarity=0.144 Sum_probs=28.1
Q ss_pred CCCCceeeeecceeEEeccCChHHHHHHHHHHHHHHHHHHhhcCCccCCCCee
Q psy10810 194 HPSLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKLENFSNDTGLFFSPQKSQ 246 (786)
Q Consensus 194 ~~~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l~~w~~~~gL~ln~~KT~ 246 (786)
.....+..|-||++|-+. +.+.+.+.....|..-|.+||-
T Consensus 331 ~~~~ti~VYGDDIIvps~-------------~a~~li~vlsyvgF~pN~kKTF 370 (561)
T PHA00028 331 GGPGTISVYGDDIIVPTE-------------VAPPLINVLSYVGFMPNLKKTF 370 (561)
T ss_pred CCCCeeEEecCceEeehh-------------hhHHHHHHHHHhceecCCcccc
Confidence 455678899999998633 2233333445789999999984
No 51
>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....
Probab=31.67 E-value=44 Score=38.54 Aligned_cols=79 Identities=15% Similarity=0.223 Sum_probs=50.3
Q ss_pred ccceeeecCcCCCCcchHHHHHHHhhcccc----cc-----CC---CCceeeeecceeEEeccCChHHHHHHHHHHHHHH
Q psy10810 162 SEDFSIVCGIPQGGVVSGTLFAIAINSITS----YI-----HP---SLSSSLFVDDFAIFTRDKNKEVLVSIMQESIDKL 229 (786)
Q Consensus 162 s~~~~~~~GvpQGs~LSPlLF~l~~~~l~~----~~-----~~---~~~~~~yADD~~i~~~~~~~~~~~~~lq~~l~~l 229 (786)
...+.+..|+|-|+++--++=+++..-+.. .+ .. .+..+.|-||.++.+...-. ....+.+
T Consensus 297 g~~y~~~~G~PSG~~~Tsi~NSi~N~i~~~~a~~~~~~~~~~~~~~~~~~i~YGDD~l~sv~~~~~-------~~n~~~i 369 (491)
T PF00680_consen 297 GKVYRVNGGNPSGSPLTSIINSIVNNIYIRYAWRKLYPDPPREFFENVKLIVYGDDNLISVPPEID-------PWNGETI 369 (491)
T ss_dssp TEEEEEESSS-TTSTTHHHHHHHHHHHHHHHHHHHHSTSCHGGGHHHSEEEEETTEEEEEESSHHH-------HHHHHHH
T ss_pred cceeeeccccccccccchhccccccceeechhhhhccccccccccceeeeeeeccccchhhhcccc-------cchhHHH
Confidence 446678899999999876543332221111 11 11 26689999999998774221 1146677
Q ss_pred HHHHhhcCCccCC-CCeeE
Q psy10810 230 ENFSNDTGLFFSP-QKSQC 247 (786)
Q Consensus 230 ~~w~~~~gL~ln~-~KT~~ 247 (786)
.+.+++.|+++.. +|+..
T Consensus 370 ~~~~~~~G~~~T~~dK~~~ 388 (491)
T PF00680_consen 370 SEFLAELGLTYTDADKTGE 388 (491)
T ss_dssp HHHHHTTTEEEEESSTSSS
T ss_pred HHHHHhcccccccccccCC
Confidence 7788889999975 88764
No 52
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=28.13 E-value=1.3e+02 Score=30.12 Aligned_cols=93 Identities=17% Similarity=0.111 Sum_probs=62.4
Q ss_pred CcccHHHHHHHHHHHHHHHHHcCCCcEEE-E----eCcHHHHHHHhccC-CCcHHHHHHHHHHhcC--CCcEEEEEecCC
Q psy10810 549 NASIFHAELFALLQSLLTIKELGACKALI-I----TDSLSCLQAITNMF-HENPLVKRVQEELSSI--EPSIEFLWCPSH 620 (786)
Q Consensus 549 ~~s~~~aEl~Ai~~aL~~~~~~~~~~i~I-~----sDs~~a~~~l~~~~-~~~~~~~~i~~~~~~~--~~~v~~~wvpgH 620 (786)
..++..+|.+|++.+|+.+...+..+.+| + .||++..+-+.+-. +...+... +...+. +....+.|+--|
T Consensus 105 ~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~--~e~~~~~~~v~h~~k~i~~~ 182 (225)
T COG3341 105 IKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD--REFFSIGKGVFHDEKDINIH 182 (225)
T ss_pred cccCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHHh--HHhhhccchhhhhhhhcccc
Confidence 45677899999999999888766555555 7 79999887776633 22111111 111111 245566788889
Q ss_pred CCCCcchHHhHHHHHHhcCCCCC
Q psy10810 621 VGIAGNEAADEEAKQAINNDVTH 643 (786)
Q Consensus 621 ~g~~~Ne~AD~lAk~a~~~~~~~ 643 (786)
.++.-+..++.++..+......+
T Consensus 183 ~~~~~~~~~~s~~~~~~k~~~~~ 205 (225)
T COG3341 183 IWIFESKKGNSHVYNTSKKELSP 205 (225)
T ss_pred cccchhhhhhhhhhchhhhhccc
Confidence 99999999988888777665443
No 53
>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=22.38 E-value=45 Score=34.56 Aligned_cols=41 Identities=17% Similarity=0.288 Sum_probs=28.4
Q ss_pred CcCCCCcchHHHHHHHhhcccccc-----------------CCCCceeeeecceeEEeccCC
Q psy10810 170 GIPQGGVVSGTLFAIAINSITSYI-----------------HPSLSSSLFVDDFAIFTRDKN 214 (786)
Q Consensus 170 GvpQGs~LSPlLF~l~~~~l~~~~-----------------~~~~~~~~yADD~~i~~~~~~ 214 (786)
|++| ||.+|+-.++..+..+ ...+.+..|.||+.|.+.+..
T Consensus 123 GLKQ----a~r~W~~~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~vYVDDili~~~~~~ 180 (246)
T PF07727_consen 123 GLKQ----APRLWYKTLDKFLKKLGFKQSKADPCLFIKKSGDGFIIILVYVDDILIAGPSEE 180 (246)
T ss_pred eccc----ccchhhhhcccccchhhhhccccccccccccccccccccccccccccccccccc
Confidence 5555 6677777777666554 124668899999999877544
No 54
>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=22.14 E-value=60 Score=32.86 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=36.4
Q ss_pred ccCCCccccchhHHHHHHhhhhhccc-----ccccccccccchhhccccc
Q psy10810 102 GIPQGGVVSGTLFAIAINSITSYIHP-----SLSSSLFVDDFAIFTRDKN 146 (786)
Q Consensus 102 Gv~qg~~~sp~l~~~~~n~l~~~~~~-----~~~~~~~~~d~~~~~~~~~ 146 (786)
-+|+|-.-||.+|..+|+.+-.-... .+...+||||.-+..+..+
T Consensus 103 ~~pFG~~~AP~~~~~~~~~~~~~~~~~~~~~~i~~~~YvDDili~~~s~~ 152 (213)
T cd01644 103 VVPFGAASAPFLANRALKQHAEDHPHEAAAKIIKRNFYVDDILVSTDTLN 152 (213)
T ss_pred EEccCCccchHHHHHHHHHHHhhcchhhHHHHHHHeeecccceecCCCHH
Confidence 68999999999999999998877764 2345689999888776644
Done!