CAARD:Cer2-3

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

(N1:0.0,Cer2:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Cer2	N1	0.3	-
Cer3	N1	0.3	-
N1	Root!	-	Cer2 Cer3

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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	0.032548	24	0.00149859	48	0.0275402	72	0.0498761
1	0.028196	25	0.000217183	49	0.00124806	73	0.000333993
2	0.0269084	26	9.06167e-005	50	0.0259827	74	0.0224481
3	0.0498761	27	0.0201276	51	0.0498761	75	0.0220105
4	0.0372241	28	0.000624535	52	0.00277478	76	0.0275402
5	0.0201276	29	0.00030487	53	0.000884248	77	0.0259827
6	0.0259827	30	0.0372241	54	0.000832469	78	0.000427678
7	0.0269084	31	0.032548	55	0.00496762	79	0.0498761
8	0.032548	32	0.0498761	56	0.000260032	80	0.0201276
9	0.00312844	33	0.00189948	57	0.000884248	81	0.028196
10	0.0297219	34	0.0498761	58	0.0283934	82	0.00141755
11	0.003304	35	0.0498761	59	0.032548	83	0.0621819
12	0.00173055	36	0.000597464	60	0.0117064	84	0.0297219
13	0.00197082	37	0.000285097	61	0.0275402	85	0.003304
14	0.0621819	38	0.032548	62	0.0269084	86	0.0621819
15	0.0347441	39	0.000484659	63	0.000934252	87	0.0330756
16	0.0498761	40	0.0118227	64	0.0498761	88	0.000992501
17	0.0621819	41	0.00496762	65	0.000638063	89	0.0275402
18	0.0498761	42	0.0498761	66	0.0141207	90	0.000870203
19	0.0259827	43	0.0297219	67	0.0118227	91	0.0275402
20	0.000428072	44	0.0372241	68	0.0330756	92	0.00173055
21	0.0283934	45	0.00496762	69	0.00405512	93	0.0224481
22	0.000342861	46	0.032548	70	0.0259827
23	0.000499456	47	0.0011501	71	0.00173055
Total log likelihood of joint reconstruction:							-453.094

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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="cer2_3" 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	0.0338425	24	0.00308282	48	0.0277081	72	0.050169
1	0.028886	25	0.000610082	49	0.00278997	73	0.000940052
2	0.0276271	26	0.000287148	50	0.0269992	74	0.0225776
3	0.050169	27	0.0205182	51	0.050169	75	0.0222665
4	0.0382672	28	0.00150921	52	0.00596595	76	0.0277081
5	0.0205182	29	0.000765612	53	0.00186039	77	0.0269992
6	0.0269992	30	0.0382672	54	0.00224015	78	0.000936449
7	0.0276271	31	0.0338425	55	0.0102288	79	0.050169
8	0.0338425	32	0.050169	56	0.000821372	80	0.0205182
9	0.00680829	33	0.0038781	57	0.00186039	81	0.028886
10	0.0307625	34	0.050169	58	0.0288953	82	0.00322796
11	0.00686751	35	0.050169	59	0.0338425	83	0.0628339
12	0.00373254	36	0.00124811	60	0.0118167	84	0.0307625
13	0.00479559	37	0.000774109	61	0.0277081	85	0.00686751
14	0.0628339	38	0.0338425	62	0.0276271	86	0.0628339
15	0.0353273	39	0.00128345	63	0.00216192	87	0.0332631
16	0.050169	40	0.0119402	64	0.050169	88	0.00219789
17	0.0628339	41	0.0102288	65	0.00139598	89	0.0277081
18	0.050169	42	0.050169	66	0.0141382	90	0.00202297
19	0.0269992	43	0.0307625	67	0.0119402	91	0.0277081
20	0.00128008	44	0.0382672	68	0.0332631	92	0.00373254
21	0.0288953	45	0.0102288	69	0.0083426	93	0.0225776
22	0.00111944	46	0.0338425	70	0.0269992
23	0.00116532	47	0.00253559	71	0.00373254
Total log likelihood of joint reconstruction:							-420.57

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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="cer2_3" 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_cer2-3 profile HMM generated consensus sequence
vDtGAnitvaskdlLKGLGdndqAvGlGGdmvvrFkiGvHFttGrCmPeieYqFiiGnD
lLskLiFvFdY

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

       Domain 1 of 1, from 1 to 70: score 36.0, E = 1.5e-11

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGA++ +v+sk+   ++k gl                      ++
AP_cer2-3      1    VDTGANI-TVASKD---LLK-GL----------------------GD 20   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 +++       + g gG++++     ++++         v++ +  G    
AP_cer2-3     21 NDQA------V-GLGGDMVV-----RFKIG--------VHFTT--G---- 44   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                        +   + ++   e     y+ I+G+ d+L++l +v +d+   
AP_cer2-3     45 -------R---C-MP-EIE-----YQFIIGN-DLLSKLIFV-FDY    70   

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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.