CAARD:TF1-2

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,TF2:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
TF2	N1	0.3	-
TF1	N1	0.3	-
N1	root!	-	TF2 TF1

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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	0.0259827	21	0.0269084	42	0.0269084	63	0.0347441
1	0.028196	22	0.0283934	43	0.0011932	64	0.0275402
2	0.0269084	23	0.0330756	44	0.0347441	65	0.0297219
3	0.0498761	24	0.0118237	45	0.0621819	66	0.0117064
4	0.0372241	25	0.000631961	46	0.000193889	67	0.0330756
5	0.0220105	26	0.00124806	47	0.0259827	68	0.0372241
6	0.00230045	27	0.0297219	48	0.00210886	69	0.0372241
7	0.0201276	28	0.032548	49	0.0621819	70	0.0259827
8	0.00496762	29	0.0259827	50	0.0201276	71	0.0297219
9	0.0259827	30	0.0224481	51	0.0498761	72	0.0275402
10	0.0269084	31	0.0498761	52	0.0259827	73	0.0269084
11	0.0358474	32	0.0498761	53	0.0297219	74	0.0269084
12	0.0358474	33	0.032548	54	0.0259827	75	0.0621819
13	0.0269084	34	0.0224481	55	0.0347441	76	0.0224481
14	0.032548	35	0.0330756	56	0.0269084	77	0.028196
15	0.0283934	36	0.000934252	57	0.0358474	78	0.0201276
16	0.0372241	37	0.0347441	58	0.0275402	79	0.0201276
17	0.0117064	38	0.0259827	59	0.0621819	80	0.0259827
18	0.0347441	39	0.0201276	60	0.032548	81	0.0358474
19	0.0621819	40	0.0283934	61	0.032548	82	0.0259827
20	0.0330756	41	0.0347441	62	0.0347441
Total log likelihood of joint reconstruction:							-316.641

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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="tf1_2" 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	0.0269992	21	0.0276271	42	0.0276271	63	0.0353273
1	0.028886	22	0.0288953	43	0.00263986	64	0.0277081
2	0.0276271	23	0.0332631	44	0.0353273	65	0.0307625
3	0.050169	24	0.0118267	45	0.0628339	66	0.0118167
4	0.0382672	25	0.00170555	46	0.000508665	67	0.0332631
5	0.0222665	26	0.00278997	47	0.0269992	68	0.0382672
6	0.0049056	27	0.0307625	48	0.00437808	69	0.0382672
7	0.0205182	28	0.0338425	49	0.0628339	70	0.0269992
8	0.0102288	29	0.0269992	50	0.0205182	71	0.0307625
9	0.0269992	30	0.0225776	51	0.050169	72	0.0277081
10	0.0276271	31	0.050169	52	0.0269992	73	0.0276271
11	0.0366289	32	0.050169	53	0.0307625	74	0.0276271
12	0.0366289	33	0.0338425	54	0.0269992	75	0.0628339
13	0.0276271	34	0.0225776	55	0.0353273	76	0.0225776
14	0.0338425	35	0.0332631	56	0.0276271	77	0.028886
15	0.0288953	36	0.00216192	57	0.0366289	78	0.0205182
16	0.0382672	37	0.0353273	58	0.0277081	79	0.0205182
17	0.0118167	38	0.0269992	59	0.0628339	80	0.0269992
18	0.0353273	39	0.0205182	60	0.0338425	81	0.0366289
19	0.0628339	40	0.0288953	61	0.0338425	82	0.0269992
20	0.0332631	41	0.0353273	62	0.0353273
Total log likelihood of joint reconstruction:							-308.435

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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="tf1_2" 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_TF profile HMM generated consensus sequence
iDtGAqvniitEEtvRAHKLPtRPWsqsviYGGvYPnKinRKtiKLninLnGisiKtEF
LvvKKFsHPAAisFttLYDnniEi

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

        Domain 1 of 1, from 1 to 83: score 43.4, E = 8.5e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTGA+v ++i++e++ a kl+                     ++P+
AP_TF          1    IDTGAQV-NIITEETVRAHKLP---------------------TRPW 25   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 s +s      + + gG ++      k++ +++k     + i ++ G    
AP_TF         26 S-QS------V-IYGGVYPN-----KINRKTIK-----LNINLN-G---- 52   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     s++++  flvv         + +   +  f + +  + i++   
AP_TF         53 ---ISIKTE--FLVV-KK------FSHPAAI-SFTTLYDNN-IEI    83   

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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.