CAARD:Micropia

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

(Blastopia:0.881961,Micropia:0.902983,Mdg3:0.704110);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Blastopia	N1	0.881961	-
Micropia	N1	0.902983	-
Mdg3	N1	0.70411	-
N1	root!	-	Blastopia Micropia Mdg3

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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	0.000120621	23	6.1784e-005	46	0.000248546	69	3.8746e-005
1	0.00505609	24	0.000164728	47	0.000454885	70	7.00993e-005
2	0.000828498	25	0.00285535	48	0.0527004	71	0.000423756
3	0.0156117	26	0.0287569	49	9.82184e-005	72	1.03041e-005
4	0.000960219	27	0.00103651	50	0.00184937	73	0.000759638
5	3.91208e-005	28	3.53772e-006	51	1.94861e-005	74	0.000124155
6	3.15652e-005	29	1.24394e-005	52	0.000733616	75	0.00106404
7	0.000828498	30	1.0724e-005	53	7.25179e-005	76	0.00041562
8	0.00106404	31	0.0156117	54	0.000441945	77	0.0156117
9	0.0035093	32	0.00228709	55	2.56027e-005	78	0.000359807
10	0.00755849	33	0.000501835	56	8.29458e-006	79	0.00217776
11	0.000216299	34	0.00027589	57	3.35713e-006	80	0.000487169
12	7.83796e-005	35	1.4141e-005	58	8.98432e-006	81	0.00223221
13	0.000766705	36	0.000114135	59	1.444e-005	82	9.10784e-005
14	1.95284e-005	37	9.45219e-005	60	0.000246635	83	3.56096e-005
15	0.000132323	38	6.73408e-006	61	0.00230475	84	9.58213e-006
16	0.000675008	39	0.000107699	62	7.50068e-005	85	0.000479756
17	7.25283e-005	40	7.41301e-006	63	0.0085868	86	0.00184858
18	5.37412e-006	41	0.000281785	64	0.00164762	87	4.2527e-006
19	2.50106e-005	42	2.69642e-005	65	0.00469993	88	4.79643e-006
20	3.95267e-005	43	0.0245309	66	2.32289e-006	89	7.32314e-006
21	1.91328e-005	44	0.000203912	67	0.000955388	90	0.000125673
22	0.00228709	45	0.000418724	68	4.87763e-005
Total log likelihood of joint reconstruction:							-775.916

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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="micropia" 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	0.000248511	23	9.17104e-005	46	0.00074098	69	0.000128453
1	0.0053195	24	0.000216649	47	0.00121157	70	8.51188e-005
2	0.00121043	25	0.0030227	48	0.091904	71	0.000498239
3	0.0156813	26	0.076748	49	0.000222311	72	2.05907e-005
4	0.00138864	27	0.0040906	50	0.00416143	73	0.000984194
5	9.13606e-005	28	1.59292e-005	51	5.58171e-005	74	0.000201166
6	6.35829e-005	29	7.10331e-005	52	0.00109903	75	0.00149388
7	0.00121043	30	2.43036e-005	53	0.000107365	76	0.00110206
8	0.00149388	31	0.0156813	54	0.00159359	77	0.0156813
9	0.00388076	32	0.0026872	55	6.94555e-005	78	0.000430033
10	0.00778119	33	0.000588708	56	3.32874e-005	79	0.0028563
11	0.000362688	34	0.000352627	57	2.49416e-005	80	0.000521539
12	0.000237267	35	6.24857e-005	58	2.43524e-005	81	0.00264051
13	0.00123557	36	0.000214597	59	6.24604e-005	82	0.000215375
14	6.12752e-005	37	0.00030198	60	0.00114713	83	0.000115294
15	0.000234473	38	1.96549e-005	61	0.00272547	84	1.54496e-005
16	0.000834352	39	0.000369435	62	0.000336954	85	0.00178059
17	0.000152418	40	2.23542e-005	63	0.022944	86	0.00219296
18	2.83785e-005	41	0.000317851	64	0.0027717	87	1.62377e-005
19	0.000114686	42	3.3452e-005	65	0.00525324	88	4.97034e-005
20	9.86311e-005	43	0.058565	66	8.00113e-006	89	4.77167e-005
21	7.18791e-005	44	0.000876904	67	0.00114109	90	0.000230245
22	0.0026872	45	0.000811997	68	0.00011893
Total log likelihood of joint reconstruction:							-707.39

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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="micropia" 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_micropia_mdg3 profile HMM generated consensus sequence
iDSGSevSiIKesIfnkmmdlaLnnTaTmlrGLGNcsvkttGQTfcyiLlkgTiqenyf
hnLfHVVhDqkmryDviiGRDfLtqcnLycsp

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

         Domain 1 of 1, from 1 to 91: score 67.0, E = 6.6e-21

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+G++v s+i+++  +++k++                     ++++
AP_micropi     1    IDSGSEV-SIIKES--IFNKMM---------------------DLAL 23   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 ++t t+    +rg  G++ +     kt+gq+         i ++ G++  
AP_micropi    24 NNTATM----LRGL-GNCSV-----KTTGQTF------CYILLK-GTI-- 54   

                 venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                   ++++ ++  f+vv+++ ++    ydvI+Gr dfL+q+n   +     
AP_micropi    55 --QENYFHNL-FHVVhDQKMR----YDVIIGR-DFLTQCNLY-CSP    91   

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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.