CAARD:Reina

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

(Reina:0.570903,Gimli:0.412249,(Gloin:0.760498,Ifg7:0.586966)N2:0.165333);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Reina	N1	0.570903	-
Gimli	N1	0.412249	-
Gloin	N2	0.760498	-
Ifg7	N2	0.586966	-
N1	root!	-	Reina Gimli N2
N2	N1	0.165333	Gloin Ifg7

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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	0.000235799	25	0.0302906	50	5.0643e-007	75	1.17796e-005
1	0.00460294	26	1.00785e-006	51	5.40004e-007	76	0.000538037
2	0.0024028	27	0.0147891	52	1.85048e-007	77	8.08168e-007
3	0.0152119	28	0.00265011	53	1.89494e-008	78	0.00460294
4	0.000677506	29	0.00019376	54	0.00826792	79	2.25499e-005
5	0.000523034	30	3.54695e-005	55	3.87171e-007	80	0.000439504
6	4.05632e-005	31	8.79597e-007	56	5.97464e-008	81	0.0188412
7	0.000410099	32	0.000520421	57	3.7813e-006	82	0.0152119
8	0.00858428	33	0.000152579	58	0.000317051	83	8.58479e-005
9	6.09975e-005	34	0.0135428	59	1.78494e-007	84	4.5467e-007
10	4.18045e-007	35	8.54883e-007	60	2.129e-007	85	0.00654592
11	3.18177e-007	36	0.00152389	61	0.0135662	86	0.000219216
12	4.03765e-007	37	0.00016696	62	2.01616e-006	87	0.000477717
13	1.39046e-005	38	9.01628e-006	63	0.000268255	88	2.94692e-006
14	3.29286e-005	39	0.0152119	64	0.0135428	89	2.39171e-006
15	1.16016e-006	40	7.78405e-008	65	2.30776e-006	90	1.10427e-005
16	0.00707594	41	1.47928e-006	66	4.41582e-005	91	6.43238e-006
17	0.0185384	42	0.000196459	67	0.000198134	92	1.37637e-005
18	2.6184e-005	43	1.54439e-008	68	8.07532e-005	93	0.0212374
19	0.00252786	44	1.48076e-006	69	1.00252e-005	94	1.82753e-007
20	0.0220053	45	1.64425e-007	70	0.0567913	95	1.4463e-005
21	1.48548e-005	46	2.59619e-006	71	4.05719e-007	96	8.9022e-009
22	3.06675e-007	47	4.69457e-006	72	0.000122069
23	2.32379e-005	48	7.93559e-005	73	0.000170413
24	0.000563793	49	0.000475973	74	0.000948396
Total log likelihood of joint reconstruction:							-971.37

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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="reina" 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	0.000418545	25	0.0307787	50	2.31439e-006	75	2.18731e-005
1	0.00466852	26	6.88579e-006	51	6.13048e-007	76	0.000548574
2	0.00245086	27	0.0148979	52	2.77983e-007	77	2.54816e-006
3	0.0152261	28	0.00675388	53	6.30962e-008	78	0.00466852
4	0.000744091	29	0.000394105	54	0.022944	79	4.01323e-005
5	0.000567586	30	0.000146515	55	7.17037e-007	80	0.000809195
6	4.11878e-005	31	2.17723e-006	56	2.23898e-007	81	0.0189099
7	0.000429429	32	0.000642537	57	9.132e-006	82	0.0152261
8	0.00859653	33	0.000169669	58	0.001587	83	0.000129976
9	0.000142834	34	1	59	2.46525e-007	84	1.4284e-006
10	1.40503e-006	35	1.75539e-006	60	4.32441e-007	85	0.00654594
11	4.08198e-007	36	0.00177465	61	0.0181871	86	0.000223509
12	8.40232e-007	37	0.000179353	62	9.06092e-006	87	0.00210078
13	7.33067e-005	38	1.56054e-005	63	0.000273318	88	3.92113e-006
14	9.49143e-005	39	0.0152261	64	1	89	1.73388e-005
15	4.10811e-006	40	3.38385e-007	65	4.01988e-006	90	2.31988e-005
16	0.00713191	41	3.13393e-006	66	6.06272e-005	91	2.68584e-005
17	0.058565	42	0.000435888	67	0.000214719	92	2.72107e-005
18	7.61232e-005	43	3.54034e-008	68	8.25345e-005	93	0.051544
19	0.00655491	44	2.30186e-006	69	1.06297e-005	94	1.43401e-006
20	0.0222284	45	6.57436e-007	70	0.091904	95	2.26221e-005
21	6.47249e-005	46	5.13199e-006	71	2.51423e-006	96	1.1491e-007
22	4.0431e-007	47	1.39039e-005	72	0.000219128
23	3.67215e-005	48	0.000201232	73	0.000173429
24	0.00165667	49	0.00161491	74	0.00103166
Total log likelihood of joint reconstruction:							-898.397

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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="reina" 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_reina profile HMM generated consensus sequence
vDSGSTHNFispqvteKltGvqsfLyPsAnaqVkVAdGrslkvkgsvpqchklkvqgnT
tFvtDFmsiPLgGiDvvLGvhWLekhttpDmnw

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

      Domain 1 of 1, from 1 to 92: score 60.3, E = 7e-19

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vD+G+++ ++is++  + +kl  ++++                + Ps
AP_reina       1    VDSGSTH-NFISPQ--VTEKLTGVQSF----------------LYPS 28   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   ++ +    +++a+G+s +      ++g+++++     ++k++ G    
AP_reina      29 --ANAQ----VKVADGRSLK------VKGSVPQC----HKLKVQ-G---- 57   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                   n+++++d  f + +++     ++dv+LG  ++L+++ ++ + +   
AP_reina      58 --NTTFVTD--F-MSIPLG----GIDVVLGV-HWLEKHTTPDMNW    92   

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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.