CAARD:Del

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

(Retrosat-2:0.508055,(Del:0.418355,Peabody:0.549836)N2:0.130960,(Tma:0.402571,(Legolas:0.242758,T32022.14:0.203860)N4:0.161988)N3:0.114301);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Retrosat-2	N1	0.508055	-
Del	N2	0.418355	-
Peabody	N2	0.549836	-
Tma	N3	0.402571	-
Legolas	N4	0.242758	-
T32022.14	N4	0.20386	-
N1	root!	-	Retrosat-2 N2 N3
N2	N1	0.13096	Del Peabody
N3	N1	0.114301	Tma N4
N4	N3	0.161988	Legolas T32022.14

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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	2.7634e-005	23	1.10388e-008	46	2.95462e-010	69	1.79097e-005
1	0.00340934	24	4.5987e-005	47	5.46282e-007	70	1.81182e-007
2	6.51993e-005	25	3.68548e-007	48	2.98556e-008	71	1.97168e-009
3	0.012882	26	4.72605e-010	49	2.01879e-005	72	1.08361e-009
4	0.00034288	27	5.28418e-010	50	6.94776e-007	73	0.000331831
5	0.000247001	28	3.51867e-010	51	2.87177e-010	74	0.000593411
6	0.00108388	29	1.78104e-011	52	3.42206e-005	75	0.000232902
7	5.78206e-007	30	3.4521e-010	53	6.62623e-010	76	0.0157214
8	0.00728457	31	3.18662e-010	54	0.000318662	77	0.012882
9	0.000215364	32	4.15036e-005	55	3.69214e-008	78	0.000992219
10	2.55547e-005	33	6.54366e-011	56	0.000116756	79	0.000405409
11	4.90025e-006	34	3.08845e-007	57	2.46362e-010	80	0.00607546
12	3.84603e-009	35	9.93104e-006	58	0.000301277	81	0.0157214
13	2.04605e-011	36	7.75457e-007	59	1.3389e-009	82	4.16937e-008
14	7.89797e-007	37	0.000278985	60	5.43052e-007	83	1.8179e-009
15	3.40311e-007	38	8.54457e-007	61	2.43292e-007	84	1.31705e-005
16	1.02062e-007	39	5.85657e-008	62	1.76841e-007	85	1.49643e-006
17	3.83996e-006	40	1.325e-006	63	0.000375865	86	2.77732e-006
18	0.0256058	41	2.83972e-011	64	0.0157214	87	2.46585e-010
19	1.20809e-005	42	1.64652e-005	65	0.000717642	88	2.13213e-006
20	8.14809e-008	43	1.80542e-009	66	1.43404e-006	89	1.83085e-005
21	2.57073e-006	44	2.95731e-007	67	6.58007e-007	90	0.00425104
22	8.98156e-008	45	0.00917882	68	4.14629e-007
Total log likelihood of joint reconstruction:							-1216.83

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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="del" 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	3.58e-005	23	4.47251e-008	46	1.71163e-009	69	1.84782e-005
1	0.00342907	24	4.98009e-005	47	2.24501e-006	70	1.96813e-007
2	0.000118185	25	3.8085e-007	48	6.66948e-008	71	1.34856e-008
3	0.0128872	26	1.31548e-009	49	2.14938e-005	72	6.23089e-009
4	0.000368313	27	2.51826e-009	50	1.1961e-006	73	0.000363925
5	0.000252836	28	3.56181e-009	51	5.11957e-010	74	0.000686706
6	0.00108462	29	1.76943e-010	52	5.39671e-005	75	0.000249252
7	1.14753e-006	30	2.1816e-009	53	1.53843e-009	76	0.0157456
8	0.00728899	31	1.59924e-009	54	0.000350446	77	0.0128872
9	0.00031009	32	4.28742e-005	55	2.98826e-007	78	0.000992838
10	3.22474e-005	33	5.4568e-010	56	0.000117233	79	0.000418738
11	4.99118e-006	34	8.69656e-007	57	1.5566e-009	80	0.00607547
12	9.63833e-009	35	1.7958e-005	58	0.00132329	81	0.0157456
13	2.63661e-010	36	1.59509e-006	59	4.25748e-009	82	1.44756e-007
14	1.2906e-006	37	0.000280208	60	1.05817e-006	83	5.82169e-009
15	4.9634e-007	38	1.45689e-006	61	6.01537e-007	84	1.34158e-005
16	1.12732e-007	39	1.19974e-007	62	5.27854e-007	85	4.19233e-006
17	2.3916e-005	40	2.84404e-006	63	0.000382615	86	4.07863e-006
18	0.058676	41	2.06724e-010	64	0.0157456	87	5.64738e-010
19	1.40461e-005	42	1.84375e-005	65	0.000772417	88	4.05002e-006
20	3.30395e-007	43	3.51732e-009	66	1.61425e-006	89	2.0148e-005
21	3.16396e-006	44	7.55317e-007	67	2.26968e-006	90	0.00425114
22	2.31437e-007	45	0.0163371	68	4.68957e-007
Total log likelihood of joint reconstruction:							-1154.91

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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="del" 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_del profile HMM generated consensus sequence
fDsGATHsFISpemvgkmgeirkeplgdpgvVnaAgGsstsvtgSvvkgvpisInGrem
paDLIilpledhDVILGMDWLakYrvvlDC

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

       Domain 1 of 1, from 1 to 89: score 77.0, E = 6.8e-24

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+GA++ s+is+e  ++ k+g+ rk                  +P+
AP_del         1    FDSGATH-SFISPE--MVGKMGEIRK------------------EPL 26   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                  ++++     + +agG+s +      ++g++ k+    v i+i+ G    
AP_del        27 GDPGV-----VNAAGGSSTS------VTGSVVKG----VPISIN-G---- 56   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                    r++p d    ++ ++ed     dvILG+ d+L ++  v  d+   
AP_del        57 ---REMPAD--LIIL-PLED----HDVILGM-DWLAKYRVV-LDC    89   

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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.