CAARD:Bel

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

(4481821:0.605843,(Bel:0.982082,(31230427:0.900315,Pao:0.876113)N3:0.154047)N2:0.104897,((31232862:0.679930,(Tas:0.849323, (cer7:1.043763,(cer10-1:0.898940,((cer8:0.668781,Cer9:0.510442)N10:0.272264,(cer12:0.195909,cer11:0.408461)N11:0.182070) N9:0.014741)N8:0.602639)N7:0.152459)N6:0.105867)N5:0.090728,((31196163:0.340113,31232486:0.504037)N13:0.083320, (31229813:0.839113,Tram:0.562567)N14:0.055101)N12:0.056849)N4:0.021543);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
4481821	N1	0.605843	-
Bel	N2	0.982082	-
31230427	N3	0.900315	-
Pao	N3	0.876113	-
31232862	N5	0.67993	-
Tas	N6	0.849323	-
cer7	N7	1.04376	-
cer10-1	N8	0.89894	-
cer8	N10	0.668781	-
Cer9	N10	0.510442	-
cer12	N11	0.195909	-
cer11	N11	0.408461	-
31196163	N13	0.340113	-
31232486	N13	0.504037	-
31229813	N14	0.839113	-
Tram	N14	0.562567	-
N1	root!	-	4481821 N2 N4
N2	N1	0.104897	Bel N3
N3	N2	0.154047	31230427 Pao
N4	N1	0.0215427	N5 N12
N5	N4	0.0907278	31232862 N6
N6	N5	0.105867	Tas N7
N7	N6	0.152459	cer7 N8
N8	N7	0.602639	cer10-1 N9
N9	N8	0.0147414	N10 N11
N10	N9	0.272264	cer8 Cer9
N11	N9	0.18207	cer12 cer11
N12	N4	0.0568487	N13 N14
N13	N12	0.08332	31196163 31232486
N14	N12	0.0551009	31229813 Tram

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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	7.24079e-013	34	6.67524e-018	68	9.25531e-015	102	1.05897e-014
1	2.68349e-009	35	2.56648e-011	69	2.12864e-012	103	1.31101e-015
2	6.78629e-018	36	3.65488e-019	70	5.26992e-013	104	1.69236e-018
3	3.30919e-011	37	1.48548e-020	71	6.56193e-012	105	5.43323e-019
4	6.80775e-013	38	4.53303e-020	72	8.6209e-010	106	1.98766e-016
5	1.63939e-016	39	1.62955e-021	73	2.65219e-014	107	1.00497e-012
6	3.25136e-021	40	5.89124e-016	74	2.15941e-013	108	5.54936e-017
7	1.03434e-015	41	9.21974e-015	75	6.10169e-018	109	3.45377e-012
8	2.35811e-019	42	7.73198e-018	76	3.87134e-017	110	1.63476e-016
9	6.7879e-014	43	5.66024e-018	77	3.29093e-021	111	1.75242e-017
10	2.09593e-010	44	4.84406e-018	78	9.93102e-015	112	7.81765e-015
11	6.17411e-018	45	3.7131e-022	79	4.81645e-019	113	1.61508e-010
12	1.94397e-019	46	2.58893e-022	80	6.89121e-021	114	6.30582e-015
13	1.04408e-016	47	2.012e-017	81	2.28779e-005	115	8.4195e-014
14	5.09335e-008	48	2.55826e-020	82	9.94124e-014	116	3.47742e-010
15	3.44399e-013	49	1.47673e-014	83	3.60274e-017	117	2.50277e-0005
16	3.13734e-019	50	2.46949e-020	84	3.54396e-022	118	1.91487e-018
17	1.51407e-018	51	3.68886e-018	85	7.47677e-025	119	1.26854e-012
18	1.31551e-013	52	2.05795e-018	86	1.28656e-014	120	1.866e-020
19	0.00638481	53	5.67067e-008	87	7.43157e-017	121	3.71025e-014
20	3.59042e-017	54	4.28831e-021	88	1.76192e-023	122	1.34089e-020
21	0.01754	55	1.60203e-021	89	5.23e-025	123	1.83162e-021
22	1.35151e-012	56	1.47567e-017	90	3.27538e-021	124	2.33163e-015
23	1.11149e-023	57	3.34195e-021	91	9.18958e-023	125	1.06646e-020
24	2.17225e-019	58	1.78885e-023	92	7.09424e-026	126	2.35218e-020
25	3.0828e-022	59	1.20206e-024	93	3.44895e-023	127	2.56223e-020
26	2.17729e-022	60	1.45963e-022	94	2.41005e-022	128	6.72408e-020
27	6.85255e-024	61	5.68431e-024	95	1.36756e-021	129	3.35338e-019
28	2.60033e-019	62	1.8189e-024	96	2.62404e-019	130	2.15279e-013
29	5.44278e-023	63	2.48176e-015	97	4.67537e-020	131	1.95258e-015
30	1.49934e-024	64	2.04719e-021	98	8.85395e-025	132	4.16501e-020
31	1.22314e-016	65	7.22613e-019	99	4.18348e-022
32	4.58009e-014	66	7.09438e-015	100	5.28986e-021
33	5.90595e-015	67	2.31307e-018	101	1.4181e-016
Total log likelihood of joint reconstruction:							-5119.68

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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="bel" 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	1.20933e-012	34	1.49619e-016	68	3.67905e-013	102	3.48661e-014
1	3.18353e-009	35	2.80475e-011	69	6.89171e-011	103	5.10143e-015
2	4.68936e-017	36	3.3949e-018	70	5.73377e-012	104	4.47252e-017
3	4.91468e-011	37	2.49775e-019	71	2.5537e-010	105	2.57809e-018
4	2.28352e-012	38	2.36324e-018	72	7.70509e-009	106	3.37011e-016
5	1.29576e-015	39	5.86935e-020	73	1.51407e-013	107	2.2831e-011
6	3.49334e-020	40	3.2562e-015	74	1.00456e-012	108	9.87034e-017
7	1.05727e-014	41	9.95213e-014	75	1.45354e-016	109	7.66121e-012
8	1.03308e-018	42	1.03583e-016	76	3.27055e-016	110	8.41827e-016
9	3.05514e-013	43	1.72577e-016	77	1.14996e-019	111	6.68686e-017
10	5.10297e-009	44	7.03409e-018	78	5.60563e-014	112	1.63216e-014
11	6.69407e-017	45	3.99522e-021	79	8.54649e-018	113	2.53941e-010
12	4.17905e-019	46	2.92391e-021	80	9.49646e-020	114	1.20777e-014
13	7.02481e-016	47	9.25281e-017	81	0.000366755	115	8.89004e-013
14	1.19722e-006	48	1.92281e-019	82	4.32825e-013	116	4.63823e-010
15	7.34026e-013	49	3.25962e-014	83	1.17017e-016	117	2.51097e-005
16	9.58329e-018	50	2.91814e-019	84	8.63672e-021	118	1.3137e-017
17	8.93173e-018	51	1.70463e-017	85	4.14766e-023	119	1.82813e-012
18	8.22776e-013	52	4.84789e-017	86	2.18976e-013	120	4.02189e-019
19	0.058676	53	1.6389e-006	87	2.7775e-015	121	1.15408e-013
20	7.93522e-017	54	7.27982e-019	88	2.46608e-021	122	5.08949e-020
21	0.091904	55	2.80801e-020	89	1.35577e-023	123	3.62168e-020
22	4.21524e-012	56	5.87536e-017	90	4.32135e-020	124	3.67156e-015
23	1.18037e-022	57	1.0556e-020	91	4.22484e-022	125	4.67236e-020
24	1.42526e-017	58	3.97277e-022	92	8.67628e-025	126	1.68928e-019
25	3.6845e-021	59	2.37544e-023	93	6.64886e-022	127	2.04828e-019
26	8.47903e-021	60	2.67693e-021	94	3.25259e-021	128	8.28625e-019
27	1.99243e-022	61	2.01123e-022	95	3.19519e-021	129	5.79831e-018
28	2.40691e-018	62	2.84222e-022	96	2.78944e-018	130	8.53888e-013
29	1.16817e-021	63	2.88751e-015	97	2.65096e-019	131	9.78542e-015
30	8.05691e-024	64	1.32177e-020	98	4.9208e-023	132	5.50002e-019
31	8.95322e-016	65	7.81395e-018	99	1.39842e-020
32	8.27644e-014	66	2.31555e-013	100	5.14462e-020
33	1.15308e-014	67	9.51129e-018	101	6.84153e-016
Total log likelihood of joint reconstruction:							-4832.94

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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="bel" 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_Bel profile HMM generated consensus sequence
DsGSqvslIterlAqqLgLkrtraslhIsgiGgnkattsksrivklsirsrnSliagle
slvltqvtaplpsnqdltdvdnwkiphneiladptfnkpgrIDiiiGnDvladllaasr

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

       Domain 1 of 1, from 1 to 119: score 62.6, E = 1.4e-19

DTG_ILG template  *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      D+G++v s+i+++  laq+lgl+r                  +++s
AP_Bel          1    -DSGSQV-SLITER--LAQQLGLKR------------------TRAS 25   

                  sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnv..
                   +        i g+gG++++ +Sk++++ +++   +s+ +++   G ++ 
AP_Bel         26 LH--------ISGIGGNKAT-TSKSRIVKLSI---RSRNSLIA--GLEsl 61   

                  ...............Tevenrslpsdgvflvvtdpedqks.rydvILGrl
                    ++ + + +++++ T+v+n+++p+++ + ++ dp ++k++r+d+I+G+ 
AP_Bel         62 vltqvtaplpsnqdlTDVDNWKIPHNE-I-LA-DPTFNKPgRIDIIIGN- 107  

                  dfLrqlnsvhidl<-*
                  d+L +l +   ++   
AP_Bel        108 DVLADLLAA-SRI    119  

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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.