CAARD:Mag

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

(Cer4:0.227252,(Gulliver:0.804526,(Mag:0.655884,SURL:0.646649)N3:0.161094)N2:0.171023,(Cigr-1:1.152764,(Cer5:0.235950,Cer6:0.207646) N5:0.142782)N4:0.016193);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Cer4	N1	0.227252	-
Gulliver	N2	0.804526	-
Mag	N3	0.655884	-
SURL	N3	0.646649	-
Cigr-1	N4	1.15276	-
Cer5	N5	0.23595	-
Cer6	N5	0.207646	-
N1	root!	-	Cer4 N2 N4
N2	N1	0.171023	Gulliver N3
N3	N2	0.161094	Mag SURL
N4	N1	0.016193	Cigr-1 N5
N5	N4	0.142782	Cer5 Cer6

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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	1.32988e-005	25	2.11241e-006	50	1.34827e-007	75	9.07489e-011
1	0.000762449	26	0.000166752	51	4.86902e-005	76	3.82289e-008
2	0.000109251	27	0.0199432	52	4.06078e-010	77	8.33098e-007
3	3.50389e-005	28	0.0220334	53	8.12997e-009	78	0.000361318
4	0.0123056	29	8.01234e-013	54	9.12806e-010	79	0.000854334
5	4.721e-005	30	2.29719e-010	55	7.44592e-007	80	0.000147356
6	1.47045e-011	31	0.000175138	56	7.83865e-006	81	0.00460652
7	2.42989e-007	32	1.53924e-007	57	0.000189816	82	1.51198e-010
8	1.93624e-005	33	1.10374e-010	58	1.14953e-006	83	6.66742e-009
9	2.2472e-007	34	8.28717e-011	59	7.28578e-005	84	0.0122317
10	2.24517e-007	35	4.69345e-014	60	8.07759e-010	85	6.64523e-007
11	3.43742e-007	36	1.93332e-008	61	3.92755e-009	86	4.47863e-008
12	1.29732e-010	37	0.0223989	62	3.1221e-008	87	5.83828e-006
13	2.58159e-011	38	1.24e-006	63	1.05636e-009	88	1.01244e-010
14	6.8833e-010	39	1.96873e-006	64	1.15034e-009	89	3.32357e-009
15	1.75258e-007	40	2.56951e-006	65	0.0115757	90	6.28565e-010
16	2.0513e-009	41	1.79752e-007	66	8.14125e-011	91	2.46668e-007
17	1.35815e-005	42	2.9916e-009	67	1.16225e-010	92	1.99655e-010
18	3.67024e-010	43	2.44301e-007	68	2.12162e-006	93	1.1576e-006
19	1.43795e-006	44	1.70486e-009	69	0.000523017	94	0.00891111
20	2.09857e-005	45	7.54047e-008	70	3.71239e-009	95	3.34396e-006
21	2.87728e-009	46	1.50341e-008	71	3.33228e-008	96	3.97525e-011
22	9.58635e-008	47	0.00460652	72	1.96354e-005	97	6.19115e-008
23	3.54282e-009	48	1.83773e-007	73	0.00201758
24	1.94628e-006	49	4.10256e-007	74	8.20494e-007
Total log likelihood of joint reconstruction:							-1487.94

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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	3.33802e-005	25	3.10537e-006	50	3.44842e-007	75	9.23118e-010
1	0.000771506	26	0.000286987	51	5.68879e-005	76	5.20718e-008
2	0.000110463	27	0.076748	52	8.25433e-010	77	9.25217e-007
3	3.51214e-005	28	0.058676	53	4.47845e-008	78	0.00159519
4	0.076748	29	6.7415e-012	54	1.98406e-009	79	0.000857662
5	5.21007e-005	30	8.5022e-010	55	1.00672e-006	80	0.000153298
6	7.70027e-011	31	0.000243101	56	7.95964e-006	81	0.00461024
7	3.89669e-007	32	1.92097e-007	57	0.000427039	82	4.46751e-010
8	3.43897e-005	33	5.18555e-010	58	1.33484e-005	83	3.80112e-008
9	2.44407e-007	34	1.87278e-010	59	7.40956e-005	84	1
10	5.01827e-007	35	1.14334e-012	60	1.2564e-009	85	6.65409e-007
11	4.25318e-007	36	5.64927e-008	61	1.72532e-008	86	7.18923e-008
12	3.43003e-010	37	0.06183	62	1.3153e-007	87	2.89723e-005
13	1.15152e-010	38	1.34986e-006	63	2.30279e-009	88	6.54461e-010
14	3.14637e-009	39	4.13861e-006	64	5.63848e-009	89	6.41678e-009
15	1.95001e-007	40	2.72294e-006	65	0.066005	90	1.17998e-009
16	9.31313e-009	41	3.9614e-007	66	5.37916e-010	91	7.4016e-007
17	1.39006e-005	42	5.00291e-009	67	8.36574e-010	92	6.74256e-010
18	7.21506e-010	43	9.42333e-007	68	2.18421e-006	93	1.64144e-006
19	2.40196e-006	44	7.08827e-009	69	0.000539592	94	0.053761
20	4.99911e-005	45	8.96987e-008	70	4.74142e-008	95	3.61824e-006
21	6.43375e-009	46	2.71808e-008	71	5.21083e-008	96	3.11996e-010
22	9.96289e-008	47	0.00461024	72	4.54413e-005	97	1.47642e-007
23	5.97957e-009	48	2.03122e-007	73	0.00430887
24	1.98095e-006	49	4.63722e-007	74	7.08561e-006
Total log likelihood of joint reconstruction:							-1401.13

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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

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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_mag profile HMM generated consensus sequence
lDTGSditlisknvweKlGkpkLeKpvphkikcAngspitvlGrcrVnfelkfGvsytd
pfYVidrgqtnLLGlsWlehspemRda

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

        Domain 1 of 1, from 1 to 86: score 57.8, E = 4.1e-18

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTG+++ ++isk+  +++klg+                    ++  
AP_mag         1    LDTGSDI-TLISKN--VWEKLGK--------------------PKL- 23   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                  k+ +   ++i++a+G+ ++      ++g++r      v +++++G    
AP_mag        24 EKPVP---HKIKCANGSPIT------VLGRCR------VNFELKFG---- 54   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     s++ d  +++v   ++   +   +LG+  +L++   +  d    
AP_mag        55 ---VSYT-D--PFYV--IDR---GQTNLLGL-SWLEHSPEM-RDA    86   

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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.