CAARD:DDI

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

(DDIDan:0.026204,((DDIan:0.117206,(DDIDro:0.181222,((DDISpom:0.233917,(DDIAni:0.148890,(DDINcra:0.091024, (DDIMgri:0.104529,DDIGzea:0.090694)N9:0.012646)N8:0.030717)N7:0.041310)N6:0.094340,((DDIAra:0.320097, ((DDIPfal:0.088877,DDIPyoe:0.059366)N13:0.215828,(DDIGlam:0.533159,DDICbri:0.712107)N14:0.201558) N12:0.054686)N11:0.048063,(DDILei:0.365656,DDICer:0.477282)N15:0.020486)N10:0.044999)N5:0.076632)N4:0.040885) N3:0.082283,(DDIMfas:0.016030,DDIMmus:0.043488)N16:0.030473)N2:0.014211,(DDIXen:0.029894, (DDIHum:0.003281,DDIRnor:0.047049)N18:0.010875)N17:0.006074);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
DDIDan	N1	0.0262037	-
DDIan	N3	0.117206	-
DDIDro	N4	0.181222	-
DDISpom	N6	0.233917	-
DDIAni	N7	0.14889	-
DDINcra	N8	0.0910241	-
DDIMgri	N9	0.104529	-
DDIGzea	N9	0.090694	-
DDIAra	N11	0.320097	-
DDIPfal	N13	0.0888766	-
DDIPyoe	N13	0.0593656	-
DDIGlam	N14	0.533159	-
DDICbri	N14	0.712107	-
DDILei	N15	0.365656	-
DDICer	N15	0.477282	-
DDIMfas	N16	0.0160301	-
DDIMmus	N16	0.0434883	-
DDIXen	N17	0.0298944	-
DDIHum	N18	0.00328061	-
DDIRnor	N18	0.047049	-
N1	root!	-	DDIDan N2 N17
N2	N1	0.0142114	N3 N16
N3	N2	0.0822829	DDIan N4
N4	N3	0.0408853	DDIDro N5
N5	N4	0.0766323	N6 N10
N6	N5	0.0943402	DDISpom N7
N7	N6	0.0413101	DDIAni N8
N8	N7	0.0307174	DDINcra N9
N9	N8	0.0126463	DDIMgri DDIGzea
N10	N5	0.0449989	N11 N15
N11	N10	0.0480625	DDIAra N12
N12	N11	0.0546856	N13 N14
N13	N12	0.215828	DDIPfal DDIPyoe
N14	N12	0.201558	DDIGlam DDICbri
N15	N10	0.0204861	DDILei DDICer
N16	N2	0.0304732	DDIMfas DDIMmus
N17	N1	0.00607407	DDIXen N18
N18	N17	0.0108746	DDIHum DDIRnor

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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	1.04031e-006	28	2.07278e-023	56	3.68473e-015	84	9.30677e-009
1	0.000458062	29	6.36391e-006	57	8.41987e-014	85	4.35605e-009
2	6.4317e-006	30	8.78508e-015	58	1.92041e-010	86	2.29823e-012
3	0.00362093	31	0.000266644	59	5.87121e-016	87	2.42343e-022
4	0.000266644	32	2.61792e-014	60	3.59782e-013	88	8.1399e-005
5	3.77022e-005	33	0.00362093	61	1.87245e-012	89	4.75546e-005
6	8.74591e-021	34	2.60946e-005	62	1.71923e-005	90	2.80043e-006
7	1.42078e-007	35	0.00362093	63	4.77374e-014	91	2.77581e-018
8	1.56597e-005	36	1.00043e-015	64	1.22011e-006	92	6.87648e-020
9	1.10588e-009	37	3.74522e-014	65	1.72592e-012	93	1.41052e-011
10	1.91651e-006	38	1.04105e-022	66	1.85957e-009	94	1.23053e-013
11	4.02458e-017	39	0.000821568	67	0.0129119	95	1.06902e-015
12	1.14558e-021	40	1.39619e-005	68	4.40964e-019	96	5.59582e-020
13	5.01139e-014	41	1.88882e-016	69	5.44922e-015	97	1.61738e-018
14	0.000266644	42	0.00362093	70	2.34288e-021	98	4.3444e-013
15	2.54724e-010	43	1.31613e-008	71	2.69674e-011	99	0.000358463
16	1.74031e-009	44	5.87569e-007	72	2.54187e-008	100	0.00818293
17	0.00138895	45	7.05116e-006	73	7.12699e-017	101	2.63019e-013
18	1.21429e-014	46	2.63437e-016	74	0.0298287	102	3.82912e-017
19	1.91153e-010	47	2.68575e-013	75	4.41244e-007	103	1.18318e-021
20	2.23125e-015	48	1.57197e-017	76	7.64903e-010	104	5.56663e-024
21	3.22196e-008	49	1.47113e-012	77	0.00362093	105	2.33609e-013
22	3.97195e-007	50	2.94586e-008	78	2.3715e-007	106	8.87572e-022
23	5.30055e-011	51	8.07382e-009	79	4.32347e-007	107	1.98135e-008
24	0.000458062	52	0.000282579	80	4.50659e-011	108	5.63882e-008
25	8.06579e-020	53	1.00739e-010	81	0.00429733	109	6.04427e-017
26	0.000472789	54	2.78009e-012	82	5.37664e-012
27	5.69615e-016	55	0.0148872	83	4.60951e-009
Total log likelihood of joint reconstruction:							-2581.74

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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="mag" 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	1.26812e-006	28	1.13383e-022	56	2.32768e-014	84	1.57364e-008
1	0.00046189	29	6.47861e-006	57	1.29608e-013	85	8.1792e-009
2	1.08606e-005	30	3.93978e-014	58	1.09949e-009	86	4.92287e-012
3	0.00362329	31	0.000268874	59	8.92643e-016	87	6.45839e-022
4	0.000268874	32	8.39643e-014	60	5.65055e-013	88	8.87457e-005
5	3.9447e-005	33	0.00362329	61	3.14878e-012	89	4.81426e-005
6	7.18311e-020	34	5.28422e-005	62	1.90804e-005	90	3.0513e-006
7	2.44681e-007	35	0.00362329	63	8.00699e-014	91	6.92704e-018
8	1.69084e-005	36	2.80447e-015	64	1.42404e-006	92	1.41283e-019
9	2.57643e-009	37	1.70641e-013	65	8.43459e-012	93	1.72979e-011
10	2.08475e-006	38	3.53471e-021	66	2.2871e-009	94	9.09753e-013
11	1.96616e-016	39	0.00403993	67	0.06183	95	5.20779e-015
12	2.19181e-020	40	1.54558e-005	68	2.74916e-018	96	4.09834e-019
13	1.17508e-013	41	2.73233e-016	69	5.53363e-014	97	3.11343e-018
14	0.000268874	42	0.00362329	70	3.43617e-020	98	4.48636e-012
15	2.75739e-010	43	2.21116e-008	71	1.02153e-010	99	0.000547417
16	3.27989e-009	44	7.10929e-007	72	5.58255e-008	100	0.0248586
17	0.001389	45	7.14359e-006	73	8.93829e-016	101	2.41183e-012
18	1.39477e-014	46	8.81337e-016	74	0.091904	102	1.23533e-016
19	5.67625e-010	47	1.04119e-012	75	5.68261e-007	103	5.0654e-021
20	3.94517e-015	48	8.13928e-017	76	3.013e-009	104	8.89264e-024
21	6.78794e-008	49	2.90448e-012	77	0.00362329	105	5.03653e-013
22	1.30172e-006	50	3.11211e-008	78	4.16717e-007	106	6.5902e-021
23	1.1207e-010	51	1.57966e-008	79	4.63536e-007	107	4.42726e-008
24	0.00046189	52	0.000999038	80	1.23649e-010	108	9.17878e-008
25	1.40591e-019	53	1.10097e-010	81	0.00430733	109	2.92644e-016
26	0.000475125	54	6.5623e-012	82	1.01129e-011
27	6.50203e-016	55	0.06183	83	9.90154e-009
Total log likelihood of joint reconstruction:							-2490.02

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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="mag" folder="mrof"></align>

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Models

Sequence Logo

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_ddi profile HMM generated consensus sequence
VDSGAQatImSkacAErCGimRLvDtRfqGiAkGVGtqkIlGrIHlaqikiGdFLpcsF
tVlEdqpmDlLLGLDmLkrHQccIDLkknllitgeetpFLp

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

      Domain 1 of 1, from 1 to 85: score 59.2, E = 1.5e-18

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vD+GA+  +++sk c  a+++g +                   ++ +
AP_ddi         1    VDSGAQA-TIMSKAC--AERCGIM-------------------RLVD 25   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 + ++        +a+G   +     k++g+i+     l  iki  G    
AP_ddi        26 T-RF------QGIAKGVGTQ-----KILGRIH-----LAQIKI--G---- 52   

                 venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                      lp++  f v++++p      +d++LG+ d+L+ ++++ idl   
AP_ddi        53 ---DFLPCS--FTVLeDQP------MDLLLGL-DMLKRHQCC-IDL    85   

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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.