CAARD:Alpharetroviridae

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

(RSV:0.363657,LPDV:0.717462,EAV-HP:0.238126);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
RSV	N1	0.363657	-
LPDV	N1	0.717462	-
EAV-HP	N1	0.238126	-
N1	root!	-	RSV LPDV EAV-HP

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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	0.00117484	22	0.0358256	44	0.000505241	66	0.0164059
1	0.01426	23	0.00166365	45	0.000823669	67	2.37143e-006
2	0.00273671	24	0.000327972	46	0.00278983	68	0.00531678
3	0.0318332	25	4.13047e-006	47	0.000254718	69	1.36305e-005
4	0.0164059	26	0.000117663	48	0.000256299	70	0.000134614
5	0.01426	27	0.028095	49	0.0116073	71	0.000137404
6	0.00277929	28	0.0052105	50	0.000433897	72	0.000673734
7	0.0110915	29	5.31937e-007	51	0.0142713	73	0.0396324
8	0.00277929	30	0.0318332	52	0.00491497	74	0.0318332
9	0.00176035	31	0.00277929	53	0.049833	75	0.0142713
10	0.00014966	32	0.0318332	54	0.0296955	76	0.00491497
11	0.0193496	33	0.0318332	55	0.000472403	77	3.15422e-006
12	1.12642e-005	34	4.8452e-005	56	0.0193496	78	0.0396324
13	9.37352e-005	35	0.0005937	57	0.00414389	79	0.00107153
14	0.0094486	36	0.000377385	58	0.000356308	80	0.0107323
15	0.0199208	37	1.57754e-005	59	2.26491e-005	81	1.30637e-005
16	5.93246e-005	38	0.000935726	60	0.000713136	82	0.000166897
17	5.23323e-005	39	0.00202355	61	0.00371725	83	0.000360101
18	0.0094486	40	0.0115495	62	1.21437e-005	84	6.35115e-005
19	0.0199208	41	7.47892e-006	63	0.0199208	85	0.0283661
20	0.00123063	42	1.1048e-005	64	5.57873e-006	86	0.00371725
21	0.0015665	43	6.40288e-006	65	0.00531678
Total log likelihood of joint reconstruction:							-597.807

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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="alpharetroviridae" 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	0.00146915	22	0.0365767	44	0.000964977	66	0.0165011
1	0.0143427	23	0.00173393	45	0.000887219	67	9.4539e-006
2	0.00289206	24	0.000692302	46	0.00491213	68	0.0057405
3	0.0318478	25	9.59089e-006	47	0.000275119	69	3.00893e-005
4	0.0165011	26	0.000159815	48	0.000269403	70	0.000136978
5	0.0143427	27	0.040752	49	0.0117445	71	0.00032452
6	0.00358495	28	0.00556649	50	0.000447465	72	0.000898795
7	0.0111468	29	1.67886e-006	51	0.0143203	73	0.039697
8	0.00358495	30	0.0318478	52	0.00517398	74	0.0318478
9	0.00276598	31	0.00358495	53	0.0501146	75	0.0143203
10	0.00025867	32	0.0318478	54	0.0306957	76	0.00517398
11	0.019458	33	0.0318478	55	0.000481192	77	6.45175e-006
12	2.20432e-005	34	7.13023e-005	56	0.019458	78	0.039697
13	0.000195066	35	0.000658171	57	0.00687743	79	0.001706
14	0.00944862	36	0.000385085	58	0.000361199	80	0.0107464
15	0.0199288	37	3.49291e-005	59	8.37657e-005	81	2.53568e-005
16	8.00944e-005	38	0.000953747	60	0.000722594	82	0.000852876
17	8.66336e-005	39	0.00237517	61	0.00381902	83	0.000364597
18	0.00944862	40	0.0116398	62	3.05705e-005	84	0.000146116
19	0.0199288	41	2.20451e-005	63	0.0199288	85	0.0288485
20	0.00139821	42	1.58606e-005	64	1.05485e-005	86	0.00381902
21	0.00272833	43	1.10597e-005	65	0.0057405
Total log likelihood of joint reconstruction:							-572.891

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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="alpharetroviridae" 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_alpharetroviridae profile HMM generated consensus sequence [hmmemit]
LDsGADvTvisEtdWPssWPaiEasqsqieGvGGatpsrrSenlvqagvInRdGSlEkp
illtPlvAavrgtiLGRdaLrQihgvRl

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

         domain 1 of 1, from 1 to 87: score 40.7, E = 5.7e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +D+GA+v +vis    + + ++                     s+P 
  AP_alphare     1    LDSGADV-TVIS----ETD-WPS--------------------SWPA 21   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    ++s   q++i g+gG ++++  +++ ++q          ++ ++G++  
  AP_alphare    22 IEAS---QSQIEGVGGATPSR--RSENLVQ--------AGVINRDGSL-- 56   

                   venrsl.psdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                      +++ + +  +lv+   +        ILGr d Lrq ++  ++l   
  AP_alphare    57 ---EKPiLLT--PLVA-AVR-----G-TILGR-DALRQIHG--VRL    87   

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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.