CAARD:Lentiviridae

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

(HIV-1:0.240948,(HIV-2:0.242190,SIVMAC:0.024963)N2:0.322066,((SIVMND:0.195084,SIVAGM:0.255789)N4:0.105710,(EIAV:0.495777, (BIV:0.687844,(FIV:0.535661,(VMV:0.195681,(SA-OMVV:0.130900,CAEV:0.176330)N9:0.030231)N8:0.233957)N7:0.158380)N6:0.032682) N5:0.209928)N3:0.023193);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
HIV-1	N1	0.240948	-
HIV-2	N2	0.24219	-
SIVMAC	N2	0.0249634	-
SIVMND	N4	0.195084	-
SIVAGM	N4	0.255789	-
EIAV	N5	0.495777	-
BIV	N6	0.687844	-
FIV	N7	0.535661	-
VMV	N8	0.195681	-
SA-OMVV	N9	0.1309	-
CAEV	N9	0.17633	-
N1	root!	-	HIV-1 N2 N3
N2	N1	0.322066	HIV-2 SIVMAC
N3	N1	0.0231928	N4 N5
N4	N3	0.10571	SIVMND SIVAGM
N5	N3	0.209928	EIAV N6
N6	N5	0.0326816	BIV N7
N7	N6	0.15838	FIV N8
N8	N7	0.233957	VMV N9
N9	N8	0.0302306	SA-OMVV CAEV

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Jpf output: Joint probability per amino acid position and total Log Likelihood

<tbody>

Position	Joint probability	Position	Joint probability	Position	Joint probability	Position	Joint probability
0	5.7476e-008	26	0.00731698	52	4.45852e-008	78	8.27202e-007
1	0.000710229	27	2.88386e-013	53	1.59508e-010	79	0.000130151
2	0.000232626	28	3.81371e-014	54	1.8688e-010	80	1.90035e-006
3	0.00475041	29	1.31587e-007	55	1.64464e-010	81	8.33775e-010
4	2.20693e-005	30	2.1178e-006	56	2.76006e-010	82	0.0155517
5	0.000710229	31	2.55684e-005	57	0.00996842	83	1.53987e-006
6	8.43787e-012	32	2.04917e-013	58	0.00983769	84	1.3617e-008
7	4.39935e-007	33	6.14377e-010	59	0.0138407	85	0.00475041
8	6.49805e-006	34	2.50307e-009	60	5.9434e-009	86	0.000726912
9	2.63725e-009	35	0.00475041	61	2.02065e-010	87	1.26968e-006
10	9.04494e-011	36	1.43748e-005	62	1.23648e-012	88	2.2475e-005
11	5.71143e-005	37	0.000148363	63	3.92614e-011	89	3.06924e-008
12	1.79819e-008	38	0.0255148	64	9.68696e-006	90	4.24072e-013
13	2.76373e-015	39	0.00475041	65	0.000626357	91	7.79496e-010
14	5.75746e-018	40	0.00818183	66	2.01639e-015	92	1.22635e-016
15	5.49705e-012	41	0.00454973	67	1.69588e-015	93	1.4552e-008
16	8.4979e-006	42	5.56131e-013	68	1.40002e-019	94	2.65282e-008
17	2.01314e-008	43	2.36297e-009	69	1.10253e-006	95	1.11407e-010
18	9.18525e-007	44	7.30644e-011	70	4.72957e-009	96	4.76167e-014
19	3.99302e-018	45	2.49677e-009	71	4.79102e-009	97	3.78883e-005
20	0.0110107	46	6.64372e-009	72	1.86631e-008	98	1.32658e-007
21	2.7288e-010	47	2.00451e-010	73	2.5724e-007	99	2.59205e-007
22	9.5127e-005	48	6.00519e-008	74	5.43415e-010	100	2.24605e-010
23	3.72236e-016	49	1.37822e-011	75	1.55809e-013	101	1.17443e-010
24	4.24771e-007	50	4.20091e-012	76	2.18557e-012	102	3.52152e-007
25	0.00688408	51	0.0101504	77	2.8037e-008
Total log likelihood of joint reconstruction:							-1821.38

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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="lentiviridae" 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	7.69272e-008	26	0.053761	52	5.02644e-008	78	1.22621e-006
1	0.000713303	27	7.88163e-013	53	4.47837e-010	79	0.000130797
2	0.000233367	28	2.34587e-013	54	5.02691e-010	80	4.77703e-006
3	0.00475182	29	1.46327e-007	55	1.90883e-010	81	2.26444e-009
4	2.23371e-005	30	3.37457e-006	56	3.00782e-010	82	0.050901
5	0.000713303	31	0.000155734	57	0.051691	83	3.26661e-006
6	8.87235e-011	32	8.45748e-013	58	0.051544	84	1.81405e-008
7	4.61081e-007	33	2.56055e-009	59	0.06183	85	0.00475182
8	8.17732e-006	34	3.69355e-009	60	4.57111e-008	86	0.000728644
9	4.40838e-009	35	0.00475182	61	5.06531e-009	87	1.86041e-006
10	7.87715e-010	36	2.22885e-005	62	2.32358e-012	88	0.00015284
11	0.000397964	37	0.000148594	63	4.58417e-011	89	4.57224e-008
12	1.47718e-007	38	0.073152	64	1.52245e-005	90	1.15574e-012
13	9.62944e-015	39	0.00475182	65	0.00297462	91	1.16483e-008
14	2.05723e-017	40	0.066005	66	4.26744e-015	92	3.55837e-016
15	1.04797e-011	41	0.042645	67	5.11101e-015	93	1.5565e-008
16	3.93375e-005	42	4.39219e-012	68	2.18894e-018	94	2.70342e-008
17	3.12146e-007	43	2.898e-009	69	1.1086e-006	95	4.74787e-010
18	7.34618e-006	44	3.89735e-010	70	4.97747e-009	96	9.87387e-014
19	5.22933e-017	45	5.91622e-009	71	2.68439e-008	97	7.10306e-005
20	0.032102	46	1.38758e-008	72	9.93937e-008	98	3.65841e-007
21	1.30578e-009	47	9.61301e-010	73	6.89278e-007	99	4.53404e-007
22	9.57315e-005	48	6.16114e-008	74	1.73143e-009	100	3.02339e-010
23	6.40125e-016	49	1.76135e-011	75	2.94412e-013	101	2.74145e-010
24	2.66435e-006	50	5.11916e-012	76	2.76138e-012	102	3.76939e-007
25	0.068765	51	0.053761	77	2.15765e-007
Total log likelihood of joint reconstruction:							-1720.76

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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="lentiviridae" 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_lentiviridae profile HMM generated consensus sequence [hmmemit]
LDTGADdtIlkthrdlklpGkpkgkiiiGIGGiikvkkydnVhveikykgkriiGtvvv
vapdtPvnilGRdnmlqkLgirLimaqL

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

          domain 1 of 1, from 1 to 82: score 50.4, E = 6.9e-16

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA+  +++++     +kl+                     ++P+
  AP_lentivi     1    LDTGADD-TILKTH--RDLKLP---------------------GKPK 23   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    k+       i g+gG+ k+     k++  ++      v+ik + G    
  AP_lentivi    24 GKI-------IIGIGGIIKV-----KKYDNVH------VEIKYK-G---- 50   

                   venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     +r +++   ++vv  p+     +  ILGr d + q+ +  i+l   
  AP_lentivi    51 --KRIIGT---VVVV-APDT----PVNILGR-DNMLQKLG--IRL    82  

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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.