Ancestral ML reconstructions were performed using FastML 2.02 (Pupko et al. 2000). The tool generates six outputs:
Name | Father | Distance to father | Sons |
HMS-Beagle | N2 | 0.330354 | - |
Yoyo | N2 | 0.297553 | - |
17.6 | N5 | 0.271949 | - |
297 | N6 | 0.251767 | - |
Tom | N6 | 0.22522 | - |
Tv1 | N7 | 0.398768 | - |
Idefix | N7 | 0.339277 | - |
Ted | N8 | 0.408362 | - |
Zam | N8 | 0.561082 | - |
Nomad | N9 | 0.459431 | - |
Burdock | N10 | 0.215663 | - |
Springer | N11 | 0.23944 | - |
Gypsyvir | N12 | 0.176204 | - |
Gypsy | N12 | 0.16905 | - |
N1 | root! | - | N2 N3 N9 |
N2 | N1 | 0.168252 | HMS-Beagle Yoyo |
N3 | N1 | 0.168457 | N4 N8 |
N4 | N3 | 0.405904 | N5 N7 |
N5 | N4 | 0.059692 | 17.6 N6 |
N6 | N5 | 0.147499 | 297 Tom |
N7 | N4 | 0.048622 | Tv1 Idefix |
N8 | N3 | 0.129785 | Ted Zam |
N9 | N1 | 0.0464883 | Nomad N10 |
N10 | N9 | 0.151782 | Burdock N11 |
N11 | N10 | 0.058741 | Springer N12 |
N12 | N11 | 0.145405 | Gypsyvir Gypsy |
Position | Joint probability | Position | Joint probability | Position | Joint probability | Position | Joint probability |
0 | 2.73491e-006 | 26 | 2.20859e-016 | 52 | 4.12105e-012 | 78 | 0.00944641 |
1 | 0.000141637 | 27 | 5.5953e-017 | 53 | 7.42747e-006 | 79 | 3.65488e-005 |
2 | 2.92433e-005 | 28 | 5.47157e-009 | 54 | 6.83881e-013 | 80 | 7.78321e-014 |
3 | 2.00053e-005 | 29 | 0.00554974 | 55 | 3.23326e-017 | 81 | 1.39678e-013 |
4 | 4.82705e-008 | 30 | 1.06009e-012 | 56 | 1.26219e-016 | 82 | 3.19738e-008 |
5 | 1.76965e-010 | 31 | 7.205e-017 | 57 | 3.40362e-008 | 83 | 7.48363e-005 |
6 | 7.19523e-010 | 32 | 8.74879e-010 | 58 | 1.28019e-014 | 84 | 1.52091e-007 |
7 | 8.55598e-008 | 33 | 1.18952e-020 | 59 | 3.59545e-015 | 85 | 6.99411e-014 |
8 | 6.11396e-012 | 34 | 1.04749e-009 | 60 | 1.03812e-011 | 86 | 1.04491e-005 |
9 | 2.92e-010 | 35 | 0.00617331 | 61 | 4.01989e-009 | 87 | 2.23165e-009 |
10 | 2.04326e-018 | 36 | 1.99809e-013 | 62 | 0.000213424 | 88 | 0.00172442 |
11 | 3.13861e-012 | 37 | 6.05687e-012 | 63 | 2.55562e-016 | 89 | 1.23558e-015 |
12 | 1.58675e-015 | 38 | 0.000124896 | 64 | 2.34014e-018 | 90 | 1.26423e-007 |
13 | 2.32747e-010 | 39 | 0.00351219 | 65 | 9.16777e-024 | 91 | 4.44034e-012 |
14 | 0.00658 | 40 | 5.56938e-015 | 66 | 9.22309e-019 | 92 | 5.88021e-005 |
15 | 2.10189e-019 | 41 | 2.68086e-007 | 67 | 6.41585e-021 | 93 | 1.11737e-013 |
16 | 5.16281e-016 | 42 | 0.000804845 | 68 | 4.84037e-018 | 94 | 9.37417e-016 |
17 | 2.50078e-017 | 43 | 0.00879857 | 69 | 4.23806e-006 | 95 | 7.43669e-015 |
18 | 1.27177e-011 | 44 | 4.95927e-013 | 70 | 0.0106926 | 96 | 1.10372e-016 |
19 | 1.48158e-010 | 45 | 6.65318e-012 | 71 | 0.0258576 | 97 | 0.00558862 |
20 | 1.59814e-015 | 46 | 3.71894e-007 | 72 | 3.15546e-005 | 98 | 4.29279e-009 |
21 | 1.89532e-013 | 47 | 9.89133e-014 | 73 | 3.06932e-005 | 99 | 1.7233e-016 |
22 | 8.67425e-019 | 48 | 4.76685e-006 | 74 | 2.86263e-013 | 100 | 2.87365e-007 |
23 | 8.79362e-006 | 49 | 7.88021e-017 | 75 | 1.29266e-009 | 101 | 1.15411e-014 |
24 | 1.19392e-005 | 50 | 9.47419e-005 | 76 | 4.62829e-011 | 102 | 7.87207e-011 |
25 | 1.42475e-017 | 51 | 5.75809e-016 | 77 | 1.65233e-020 | ||
Total log likelihood of joint reconstruction: | -2433.38 |
There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="errantiviridae3" folder="jrof"></align>
Position | Joint probability | Position | Joint probability | Position | Joint probability | Position | Joint probability |
0 | 2.87274e-006 | 26 | 9.12321e-016 | 52 | 1.09761e-011 | 78 | 0.058676 |
1 | 0.000142921 | 27 | 1.69004e-016 | 53 | 9.00845e-005 | 79 | 3.85878e-005 |
2 | 2.94429e-005 | 28 | 8.00653e-008 | 54 | 2.13425e-012 | 80 | 2.0354e-013 |
3 | 2.03323e-005 | 29 | 0.058565 | 55 | 2.66264e-015 | 81 | 5.03438e-013 |
4 | 1.33302e-007 | 30 | 1.9785e-012 | 56 | 1.02019e-015 | 82 | 7.95216e-008 |
5 | 4.17371e-010 | 31 | 1.07869e-015 | 57 | 1.15428e-007 | 83 | 7.62803e-005 |
6 | 1.23558e-009 | 32 | 3.18943e-009 | 58 | 3.4691e-013 | 84 | 1.61364e-007 |
7 | 1.65518e-007 | 33 | 1.08699e-019 | 59 | 3.24599e-014 | 85 | 1.28105e-013 |
8 | 2.04006e-011 | 34 | 2.53163e-009 | 60 | 6.14257e-011 | 86 | 1.17027e-005 |
9 | 4.40765e-010 | 35 | 0.076748 | 61 | 1.08979e-007 | 87 | 2.8583e-009 |
10 | 2.15072e-017 | 36 | 4.06744e-013 | 62 | 0.000561817 | 88 | 0.00172555 |
11 | 5.42116e-012 | 37 | 1.40157e-011 | 63 | 3.14475e-016 | 89 | 7.61517e-015 |
12 | 9.36008e-015 | 38 | 0.000126504 | 64 | 1.12392e-017 | 90 | 1.43029e-007 |
13 | 5.81735e-009 | 39 | 0.042645 | 65 | 1.11673e-022 | 91 | 1.10078e-011 |
14 | 0.066005 | 40 | 3.47183e-014 | 66 | 7.51499e-018 | 92 | 6.17812e-005 |
15 | 1.60065e-018 | 41 | 8.9673e-007 | 67 | 5.57004e-019 | 93 | 3.75948e-013 |
16 | 6.95682e-015 | 42 | 0.0103865 | 68 | 1.42412e-017 | 94 | 3.00992e-015 |
17 | 1.73244e-016 | 43 | 0.0345596 | 69 | 6.64938e-005 | 95 | 1.16281e-014 |
18 | 1.92441e-011 | 44 | 1.58275e-012 | 70 | 0.058676 | 96 | 4.21128e-016 |
19 | 6.49989e-009 | 45 | 1.10513e-011 | 71 | 0.091904 | 97 | 0.040752 |
20 | 5.45467e-015 | 46 | 2.08709e-005 | 72 | 3.17935e-005 | 98 | 9.56084e-009 |
21 | 9.51639e-013 | 47 | 1.59945e-012 | 73 | 9.47168e-005 | 99 | 1.36285e-015 |
22 | 2.49386e-017 | 48 | 3.67835e-005 | 74 | 7.40621e-013 | 100 | 3.9867e-007 |
23 | 0.000206364 | 49 | 1.89877e-016 | 75 | 2.62746e-009 | 101 | 4.26779e-014 |
24 | 0.000169346 | 50 | 0.00138433 | 76 | 5.21358e-011 | 102 | 9.76675e-011 |
25 | 3.76171e-017 | 51 | 4.80593e-015 | 77 | 3.00597e-019 | ||
Total log likelihood of joint reconstruction: | -2282.45 |
There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. <align id="errantiviridae3" folder="mrof"></align>
Sequence logo constructed from the input of the processed Jrof alignment. In every position, each residue is a letter whose height is proportional to its frequency multiplied by the information content of each position measured in bits. Letters are placed such that the most common is at the top.
The logo was constructed using ChekAlign server with the Shannon's algorithm (Shannon 1997) and options "include gaps" and "Correction factor". Gaps are not represented by any symbol but occupy a blank also proportional to its frequency and, for aesthetic reasons, always at the top. Maximum entropy is log221. The alignment gap is considered to be another state or amino acid species.
>AP_errantiviridae profile HMM generated consensus sequence IDTGSnkNyIrpnllklpvqntfsVttihGitlkrslnipskfntteqFFlLhslssyF DglIGrdlLkqaeAkidl
Domain 1 of 1, from 1 to 77: score 43.4, E = 8.7e-14 DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs +DTG++ + i ++ ++kl P AP_erranti 1 IDTGSNK-NYIRPN---LLKL------------------------PV 19 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe ++t+ +++++G++ + +++ + k + AP_erranti 20 QNTFS-----VTTIHGITLK-----RSLN---------IPSKFN-T---- 45 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-* +++ f+++++++ ++d+++Gr d+L+q++++ idl AP_erranti 46 ------TEQ--FFLLHSLSS---YFDGLIGR-DLLKQAEAK-IDL 77
Llorens, C. Futami, R. Renaud, G. and A. Moya (2009). Bioinformatic Flowchart and Database to Investigate the Diversity of Clan AA Peptidases.Biology Direct, 4:3.
Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061