CAARD:Errantiviridae

Welcome to the CAARD

The Clan AA Reference Database (CAARD), an in-progress database developed to investigate the major consensus and the phylogeny of clan AA to typify the different protein families according to prior (and further) estimations of their relationships using phylogenies, ancestral reconstructions, sequence logos and HMMs.

Ancestral Maximum Likelihood (ML) Joint Reconstruction

Comments

Ancestral ML reconstructions were performed using FastML 2.02 (Pupko et al. 2000). The tool generates six outputs:

• Pin; reconstructed ancestral NJ tree in newick format.
• Fin; parental relationship among reconstructed nodes and contemporary sequences.
• Jrof; multiple alignment of contemporary sequences and nodes reconstructed with the Joint method.
• Jpf; joint probability per position and total log likelihood.
• Mrof; multiple alignment of contemporary sequences and nodes reconstructed with the marginal method
• Mpf; marginal probability and total log likelihood

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Pin output : Ancestral tree

(((HMS-Beagle:0.330354,Yoyo:0.297553)N2:0.168252,(((17.6:0.271949,(297:0.251767,Tom:0.225220)N6:0.147499)N5:0.059692, (Tv1:0.398768,Idefix:0.339277)N7:0.048622)N4:0.405904,(Ted:0.408362,Zam:0.561082)N8:0.129785)N3:0.168457,(Nomad:0.459431, (Burdock:0.215663,(Springer:0.239440,(Gypsyvir:0.176204,Gypsy:0.169050)N12:0.145405)N11:0.058741)N10:0.151782)N9:0.046488);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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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

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Jpf output: Joint probability per amino acid position and total Log Likelihood

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

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Jrof output: Ancestral ML Reconstruction Alignment

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>

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Mpf output: Marginal probability per amino acid position and total Log Likelihood

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

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Mrof output: Ancestral ML Reconstruction Alignment

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>

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Models

Sequence Logo

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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.

• Basic residues are represented in red
• Hydrophobic residues in black
• Amino acids frequent in β-turns (G and P) in dark grey
• Small nucleophiles in violet
• Acidic residues in orange
• Acidic-relative amides in green

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.

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HMMs

>AP_errantiviridae profile HMM generated consensus sequence
IDTGSnkNyIrpnllklpvqntfsVttihGitlkrslnipskfntteqFFlLhslssyF
DglIGrdlLkqaeAkidl

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Pairwise alignment between the MRC sequence and the DTG/ILG template HMM-profile

        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   

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Cite this site

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.