CAARD:Osvaldo

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

(Osvaldo:0.539548,Woot:0.784602,(Ulysses:0.951997,Circe:0.884199)N2:0.116174);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Osvaldo	N1	0.539548	-
Woot	N1	0.784602	-
Ulysses	N2	0.951997	-
Circe	N2	0.884199	-
N1	root	-	Osvaldo Woot N2
N2	N1	0.116174	Ulysses Circe

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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	6.38835e-005	26	0.00210045	52	2.70309e-007	78	9.6582e-006
1	0.0023797	27	1.03345e-005	53	7.96031e-008	79	8.19153e-005
2	0.000354121	28	2.52451e-005	54	6.24469e-005	80	1.83302e-006
3	0.00953299	29	6.34333e-007	55	0.000854223	81	9.63664e-006
4	0.000437991	30	1.1538e-006	56	0.0172886	82	1.76599e-005
5	1.06819e-005	31	1.54142e-005	57	0.0150888	83	8.38261e-007
6	1.61515e-006	32	3.92257e-006	58	2.18945e-005	84	1.78623e-006
7	0.000978108	33	0.000610633	59	0.000275988	85	3.31788e-005
8	1.05209e-006	34	0.0188969	60	5.26161e-006	86	3.60613e-006
9	0.000466986	35	1.27428e-005	61	3.66838e-006	87	4.03496e-006
10	0.000696864	36	3.45382e-007	62	0.000164983	88	7.92777e-007
11	6.05514e-005	37	2.60106e-006	63	4.06809e-006	89	0.0119681
12	9.23008e-006	38	4.31271e-005	64	1.40584e-006	90	0.00953299
13	0.00221601	39	2.9558e-006	65	3.3051e-006	91	6.07395e-007
14	1.41029e-006	40	0.00191219	66	2.13816e-006	92	0.0023797
15	1.96043e-007	41	9.02629e-006	67	1.84451e-005	93	3.17622e-007
16	9.90071e-005	42	0.0171471	68	0.000884911	94	0.000114144
17	0.0251626	43	9.82949e-006	69	0.0150888	95	1.93093e-007
18	0.0119681	44	1.15808e-007	70	0.025644	96	5.20809e-006
19	3.69258e-006	45	3.62039e-006	71	0.0187838	97	2.7953e-008
20	1.09397e-005	46	0.0001786	72	0.025644	98	7.72173e-005
21	0.000716668	47	3.49775e-005	73	0.0217892	99	1.99612e-005
22	3.59712e-007	48	0.000113629	74	2.85709e-007	100	1.50504e-006
23	0.000249906	49	7.10232e-006	75	1.21387e-006	101	1.0596e-008
24	1.61077e-008	50	2.10223e-006	76	0.000139723	102	0.000125863
25	1.61305e-005	51	1.21054e-006	77	1.44954e-005	103	3.45242e-005
Total log likelihood of joint reconstruction:							-1084.06

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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="osvaldo" 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	0.000212012	26	0.00476742	52	5.42476e-007	78	5.33744e-005
1	0.00244121	27	5.78801e-005	53	5.48693e-007	79	0.000357736
2	0.000395807	28	9.26706e-005	54	0.00012425	80	2.10075e-006
3	0.00954675	29	1.89013e-006	55	0.000995906	81	2.38773e-005
4	0.000495857	30	4.3183e-006	56	0.058565	82	6.43551e-005
5	1.99486e-005	31	4.06309e-005	57	0.040752	83	4.29485e-006
6	4.30916e-006	32	2.66641e-005	58	3.22459e-005	84	3.17468e-006
7	0.00101967	33	0.00328228	59	0.000490331	85	0.00011094
8	2.4731e-006	34	0.051691	60	1.18047e-005	86	6.07591e-006
9	0.000536418	35	4.62778e-005	61	4.63027e-006	87	5.83355e-006
10	0.00108977	36	1.40815e-006	62	0.000261745	88	1.71686e-006
11	0.000154882	37	7.03487e-006	63	4.90705e-006	89	0.0120418
12	1.87138e-005	38	4.55547e-005	64	2.55912e-006	90	0.00954675
13	0.00262301	39	5.08916e-006	65	1.35244e-005	91	2.45132e-006
14	2.47417e-006	40	0.00196574	66	7.27919e-006	92	0.00244121
15	7.83229e-007	41	1.08075e-005	67	3.90966e-005	93	3.73539e-007
16	0.000138113	42	0.0173238	68	0.00292819	94	0.00011694
17	0.06183	43	1.35766e-005	69	0.040752	95	8.46518e-007
18	0.0120418	44	7.94778e-007	70	0.058676	96	9.37867e-006
19	5.75025e-006	45	6.29069e-006	71	0.068765	97	1.23877e-007
20	2.19538e-005	46	0.000523866	72	0.058676	98	0.000156668
21	0.00291952	47	7.4824e-005	73	0.040126	99	3.66765e-005
22	2.03558e-006	48	0.000146631	74	1.17621e-006	100	3.9861e-006
23	0.000257553	49	1.11903e-005	75	4.34923e-006	101	5.33114e-008
24	8.38816e-008	50	5.16133e-006	76	0.000168386	102	0.000157264
25	5.07155e-005	51	4.49546e-006	77	2.41623e-005	103	4.39289e-005
Total log likelihood of joint reconstruction:							-1001.92

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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="osvaldo" 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_osvaldo profile HMM generated consensus sequence
lDTGAsvSlISgeLakrLiektGfeptfasmtriRgAnGqcsevgtqlypkirfgsrqy
ldvvlvmcpnpviddlvLGiDfLagmgtaidf

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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 64.7, E = 3.3e-20

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTGAsv s+is e  la++l ++++                  +P 
AP_osvaldo     1    LDTGASV-SLISGE--LAKRLIEKTG-----------------FEP- 26   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 + +s+t+   irga+Gq ++       +g+       ++  ki++G    
AP_osvaldo    27 TFASMTR---IRGANGQ-CS------EVGT-------QLYPKIRFG---- 55   

                 venrslpsdgvflvvtdpedqks.rydvILGrldfLrqlnsvhidl<-*
                   +r ++ d  +++v++p+   +   d++LG+ dfL  +++  id+   
AP_osvaldo    56 --SRQYL-D--VVLVMCPN---PvIDDLVLGI-DFLAGMGTA-IDF    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.