CAARD:Gammaretroviridae

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

(FeLV:0.074252,(BAEVM:0.177409,((Herv.E:0.330059,RTVL.H3:0.397258)N4:0.043729,((MdEV:0.117158,(KorV:0.051457,GALV:0.041148)N7:0.023153) N6:0.106950,(PERV.MSL:0.162721,(Q88269:0.335537,REV:0.226503)N9:0.044583)N8:0.024222)N5:0.040673)N3:0.035644)N2:0.051896, (CHO.K1:0.122359,MuLV:0.079455)N10:0.006934);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
FeLV	N1	0.0742518	-
BAEVM	N2	0.177409	-
Herv.E	N4	0.330059	-
RTVL.H3	N4	0.397258	-
MdEV	N6	0.117158	-
KorV	N7	0.0514574	-
GALV	N7	0.0411484	-
PERV.MSL	N8	0.162721	-
Q88269	N9	0.335537	-
REV	N9	0.226503	-
CHO.K1	N10	0.122359	-
MuLV	N10	0.0794548	-
N1	root!	-	FeLV N2 N10
N2	N1	0.0518959	BAEVM N3
N3	N2	0.035644	N4 N5
N4	N3	0.0437293	Herv.E RTVL.H3
N5	N3	0.0406726	N6 N8
N6	N5	0.10695	MdEV N7
N7	N6	0.0231535	KorV GALV
N8	N5	0.0242217	PERV.MSL N9
N9	N8	0.044583	Q88269 REV
N10	N1	0.00693423	CHO.K1 MuLV

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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	7.0903e-006	17	2.06774e-013	34	3.02075e-012	51	0.00843806
1	0.00409784	18	7.15108e-010	35	1.36025e-009	52	1.14077e-013
2	0.00225569	19	2.04809e-015	36	1.69932e-016	53	0.00843806
3	0.000643944	20	2.53548e-012	37	0.000255183	54	0.0179303
4	0.00369529	21	3.59202e-017	38	1.98331e-008	55	0.0179303
5	3.18526e-011	22	0.0148059	39	7.03591e-016	56	0.000349375
6	0.001388	23	6.82992e-006	40	4.92131e-005	57	0.00421309
7	5.01132e-005	24	1.32317e-008	41	1.83262e-008	58	0.0003562
8	0.000127597	25	0.0148059	42	0.001388	59	0.000895871
9	2.04489e-005	26	2.70036e-009	43	2.20665e-005	60	0.0179303
10	3.71639e-015	27	7.62572e-007	44	0.0083459	61	1.34406e-008
11	7.06709e-020	28	1.39203e-018	45	0.0179303	62	0.00653438
12	5.66295e-010	29	1.01238e-010	46	1.58679e-012	63	0.000263054
13	7.01289e-006	30	9.11851e-013	47	5.15942e-007	64	7.15299e-014
14	9.60083e-013	31	1.12326e-010	48	0.00843806	65	1.10447e-006
15	3.14686e-011	32	2.84939e-006	49	2.48944e-008	66	4.75669e-010
16	2.13334e-015	33	2.47728e-009	50	0.00485142	67	1.62086e-005
Total log likelihood of joint reconstruction:							-1116.14

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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="gammaretroviridae" 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	7.51965e-006	17	6.17775e-013	34	5.70703e-012	51	0.00843862
1	0.00410181	18	1.04178e-009	35	1.42824e-009	52	3.41556e-013
2	0.00225731	19	6.31039e-015	36	2.37055e-016	53	0.00843862
3	0.000648327	20	5.65637e-012	37	0.000257423	54	0.0179351
4	0.00369849	21	4.02912e-016	38	2.76715e-008	55	0.0179351
5	4.0397e-011	22	0.014807	39	2.1986e-015	56	0.000350442
6	0.00138817	23	6.99298e-006	40	4.97564e-005	57	0.00421537
7	5.03437e-005	24	1.44632e-008	41	2.75158e-008	58	0.00035981
8	0.000129386	25	0.014807	42	0.00138817	59	0.000903306
9	2.0931e-005	26	1.52431e-008	43	2.23159e-005	60	0.0179351
10	1.0065e-014	27	1.07891e-006	44	0.0083468	61	3.19135e-008
11	1.79617e-019	28	3.1275e-018	45	0.0179351	62	0.0065381
12	6.05901e-010	29	3.30667e-010	46	1.90698e-012	63	0.000264099
13	7.03905e-006	30	3.63885e-012	47	7.51521e-007	64	2.32844e-013
14	1.12063e-012	31	1.55851e-010	48	0.00843862	65	1.12541e-006
15	3.3123e-011	32	3.46562e-006	49	5.77459e-008	66	1.69647e-009
16	3.80101e-015	33	3.70343e-009	50	0.00485144	67	1.65441e-005
Total log likelihood of joint reconstruction:							-1091.89

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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="gammaretroviridae" 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_gammaretroviridae profile HMM generated consensus sequence
vDtgAeHsvltqpplssktaviGatGqkqypwttkvqlgkvtHsFLviPecPlPLLgRd
lLtKLkaqi

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

        Domain 1 of 1, from 1 to 68: score 45.0, E = 2.8e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGA++ sv++       + +                        s
AP_gammare     1    VDTGAEH-SVLT-------QPP-----------------------LS 16   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 skt       + ga Gq+++       +++        +++++  G    
AP_gammare    17 SKTA------VIGATGQKQY-------PWT--------TKVQL--G---- 39   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     + +++  flv+  pe+    +  +LGr d+L++l+    ++   
AP_gammare    40 ----KVTHS--FLVI--PEC----PLPLLGR-DLLTKLK---AQI    68   

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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.