CAARD:Athila

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

(Athila-4:0.340501,(BAB61168.1:0.075102,Rigy-2:0.141744)N2:0.272239,((VfCiclops2:0.320751,(Calypso2-1:0.331080,Ciclops1:0.367491) N5:0.092515)N4:0.081529,(Diaspora:0.377623,Bagy-2:0.660810)N6:0.060058)N3:0.055184);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Athila-4	N1	0.340501	-
BAB61168.1	N2	0.0751018	-
Rigy-2	N2	0.141744	-
VfCiclops2	N4	0.320751	-
Calypso2-1	N5	0.33108	-
Ciclops1	N5	0.367491	-
Diaspora	N6	0.377623	-
Bagy-2	N6	0.66081	-
N1	root!	-	Athila-4 N2 N3
N2	N1	0.272239	BAB61168.1 Rigy-2
N3	N1	0.0551835	N4 N6
N4	N3	0.081529	VfCiclops2 N5
N5	N4	0.0925146	Calypso2-1 Ciclops1
N6	N3	0.0600579	Diaspora Bagy-2

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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	1.41103e-008	28	2.46677e-008	56	2.96975e-006	84	0.0008017
1	0.000153471	29	2.70871e-008	57	3.66155e-005	85	0.00969646
2	0.000660474	30	4.51993e-010	58	2.58898e-013	86	0.00221299
3	0.00969646	31	1.05028e-006	59	5.98165e-010	87	4.95743e-005
4	0.000174454	32	6.23812e-008	60	6.85636e-008	88	0.0055099
5	0.000845527	33	5.05453e-005	61	1.06454e-009	89	2.28789e-006
6	7.61164e-005	34	1.01623e-008	62	1.34963e-005	90	5.3973e-011
7	1.87858e-005	35	0.000381859	63	2.25911e-006	91	0.000127219
8	3.44164e-008	36	0.000116999	64	3.85403e-006	92	5.82306e-007
9	1.28012e-005	37	2.5479e-005	65	0.00217532	93	5.63143e-009
10	7.09691e-005	38	4.58245e-009	66	0.0055099	94	2.82072e-010
11	5.55139e-007	39	0.000379158	67	1.75343e-007	95	5.90529e-012
12	2.11433e-006	40	8.93302e-008	68	0.000316625	96	1.44325e-006
13	3.83534e-007	41	7.12186e-006	69	1.58809e-005	97	0.00217532
14	1.80537e-009	42	1.15613e-010	70	2.6882e-007	98	5.63261e-007
15	3.01972e-009	43	8.16557e-011	71	5.74721e-006	99	1.65073e-013
16	0.000278798	44	1.58488e-006	72	0.0262061	100	3.56282e-010
17	0.00276511	45	2.44936e-013	73	0.019936	101	6.8098e-007
18	2.35899e-007	46	2.65118e-007	74	0.000225562	102	1.07735e-010
19	0.0154243	47	4.32562e-009	75	8.16879e-009	103	6.6331e-008
20	0.020775	48	0.0155082	76	1.01208e-010	104	5.04012e-012
21	0.000991446	49	0.0154243	77	4.28167e-008	105	4.10705e-005
22	7.99039e-006	50	8.0316e-011	78	1.85779e-010	106	9.51988e-008
23	6.3989e-013	51	2.02958e-005	79	1.01433e-011	107	2.12039e-011
24	8.90299e-008	52	3.11841e-008	80	7.55338e-012	108	1.48121e-008
25	2.59012e-008	53	4.06293e-011	81	0.000131361	109	1.09217e-005
26	5.25571e-008	54	2.41888e-011	82	2.09607e-006
27	6.50451e-011	55	1.90212e-006	83	0.00119786
Total log likelihood of joint reconstruction:							-1596.59

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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="mag" 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	1.57661e-008	28	3.58714e-008	56	5.11101e-006	84	0.000809144
1	0.000155314	29	2.80941e-008	57	0.000115077	85	0.00969912
2	0.000667868	30	2.01694e-009	58	8.10242e-013	86	0.00221753
3	0.00969912	31	2.06014e-006	59	1.85868e-009	87	4.97412e-005
4	0.000180199	32	8.68025e-008	60	7.18354e-008	88	0.00551211
5	0.000849147	33	0.000103165	61	1.83493e-009	89	4.09398e-006
6	0.000145701	34	1.22417e-008	62	1.6215e-005	90	2.18778e-010
7	2.64505e-005	35	0.000385048	63	2.28222e-006	91	0.000132107
8	1.43806e-007	36	0.000120672	64	4.03156e-006	92	6.25873e-007
9	1.30195e-005	37	4.88928e-005	65	0.00218325	93	7.39581e-009
10	7.15841e-005	38	9.61962e-009	66	0.00551211	94	1.02857e-009
11	5.63979e-007	39	0.00232884	67	2.49697e-007	95	1.09684e-011
12	2.46581e-006	40	9.80526e-008	68	0.000341949	96	1.56714e-006
13	1.00673e-006	41	1.13577e-005	69	2.84738e-005	97	0.00218325
14	6.55359e-009	42	4.33337e-010	70	3.62316e-007	98	8.53786e-007
15	8.89954e-009	43	9.86113e-011	71	5.8495e-006	99	4.57982e-013
16	0.00166947	44	1.61748e-006	72	0.06183	100	4.64375e-010
17	0.00656887	45	1.30593e-012	73	0.051544	101	7.18962e-007
18	6.15311e-007	46	2.67716e-007	74	0.0010497	102	1.84261e-010
19	0.051544	47	1.53891e-008	75	2.8875e-008	103	1.69063e-007
20	0.06183	48	0.051691	76	2.21892e-010	104	1.8105e-011
21	0.00100016	49	0.051544	77	1.06715e-007	105	0.000207565
22	8.11939e-006	50	3.29317e-010	78	4.62272e-010	106	3.15735e-007
23	9.96076e-012	51	2.06326e-005	79	7.87047e-011	107	6.04734e-011
24	1.80339e-007	52	3.29089e-008	80	4.46564e-011	108	7.64425e-008
25	3.18153e-008	53	1.45662e-010	81	0.000131713	109	1.10654e-005
26	1.0047e-007	54	2.86689e-011	82	4.64204e-006
27	1.57683e-010	55	2.19862e-006	83	0.00120696
Total log likelihood of joint reconstruction:							-1529.38

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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="mag" 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_athila profile HMM generated consensus sequence
iDLGAsvsvmPlsiykrLgstelqstrmtlqLADrsvryPyGiiEDmLvKidkFvfPvD
FvvLDmdeekeiPLiLGRPFlstAgAniDvEkGsi

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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 54.2, E = 4.8e-17

DTG_ILG template*->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                   +D GAsv sv++ +  + ++lg                     ++  
AP_athila     1    IDLGASV-SVMPLS--IYKRLGS--------------------TEL- 23   

                sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                + t +t    ++ a+ + ++      ++g i++     + +ki+k     
AP_athila    24 QSTRMT----LQLADRSVRY------PYGIIED-----MLVKIDKF---- 54   

                venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     ++ d  f+v+ d++ +k+ +++ILGr +fL+ ++++ id+   
AP_athila    55 ---VFPV-D--FVVL-DMDEEKE-IPLILGR-PFLSTAGAN-IDV    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.