CAARD:DTG/ILG Template

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

Top

Pin output : Ancestral tree

(((Copia:0.916936,Osvaldo:0.563301)N3:0.146182,((Cer1:0.829200,Ty3:0.890251)N5:0.184928,(Csrn1:0.528883,Athila:0.652479) N6:0.094564)N4:0.071621)N2:0.102213,(((Deltaretro:0.543880,MuERV-L:0.496865)N9:0.132274,(Alpharetro:0.574906, (Betaretrov:0.547874,(Lentivirid:0.494975,Spumaretro:0.821320)N12:0.093139)N11:0.021775)N10:0.076297)N8:0.113606, (Saspease:0.728291,(Bel:0.745244,(TF:0.882263,(412_mdg1:0.591421,Micropia_m:0.658472)N16:0.064278)N15:0.073309) N14:0.077721)N13:0.019277)N7:0.038793,((((Pep_a1_D2:0.461136,(Pep_a1_D1:0.329115,(Pep_a2_D1:0.492369,(Pep_a2_D2:0.737344, Bs1:1.152137)N23:0.333776)N22:0.233599)N21:0.238258)N20:0.294803,(WdSV:0.726469,(Caulimovir:0.675504,Cer2-3:0.611622) N25:0.063405)N24:0.061447)N19:0.057159,((DDI:0.386312,NIX:0.823758)N27:0.310560,(Tat:0.704555,(Galadriel:0.665683, ((Mag:0.512703,Crm:0.909941)N31:0.144802,(Del:0.574016,(Reina:0.540957,Chrofung:0.452892)N33:0.172630)N32:0.025520) N30:0.060314)N29:0.034016)N28:0.050986)N26:0.032054)N18:0.051203,((Errrativir:0.609310,COG5550:0.609221)N35:0.196395, (Gammaretro:0.462520,COG3577:0.759380)N36:0.092148)N34:0.031991)N17:0.003688);

Top

Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide

Name	Father	Distance to father	Sons
Copia	N3	0.916936	-
Osvaldo	N3	0.563301	-
Cer1	N5	0.8292	-
Ty3	N5	0.890251	-
Csrn1	N6	0.528883	-
Athila	N6	0.652479	-
Deltaretro	N9	0.54388	-
MuERV-L	N9	0.496865	-
Alpharetro	N10	0.574906	-
Betaretrov	N11	0.547874	-
Lentivirid	N12	0.494975	-
Spumaretro	N12	0.82132	-
Saspease	N13	0.728291	-
Bel	N14	0.745244	-
TF	N15	0.882263	-
412_mdg1	N16	0.591421	-
Micropia_m	N16	0.658472	-
Pep_a1_D2	N20	0.461136	-
Pep_a1_D1	N21	0.329115	-
Pep_a2_D1	N22	0.492369	-
Pep_a2_D2	N23	0.737344	-
Bs1	N23	1.15214	-
WdSV	N24	0.726469	-
Caulimovir	N25	0.675504	-
Cer2-3	N25	0.611622	-
DDI	N27	0.386312	-
NIX	N27	0.823758	-
Tat	N28	0.704555	-
Galadriel	N29	0.665683	-
Mag	N31	0.512703	-
Crm	N31	0.909941	-
Del	N32	0.574016	-
Reina	N33	0.540957	-
Chrofung	N33	0.452892	-
Errrativir	N35	0.60931	-
COG5550	N35	0.609221	-
Gammaretro	N36	0.46252	-
COG3577	N36	0.75938	-
N1	root!	-	N2 N7 N17
N2	N1	0.102213	N3 N4
N3	N2	0.146182	Copia Osvaldo
N4	N2	0.071621	N5 N6
N5	N4	0.184928	Cer1 Ty3
N6	N4	0.094564	Csrn1 Athila
N7	N1	0.038793	N8 N13
N8	N7	0.113606	N9 N10
N9	N8	0.132274	Deltaretro MuERV-L
N10	N8	0.0762969	Alpharetro N11
N11	N10	0.0217751	Betaretrov N12
N12	N11	0.0931393	Lentivirid Spumaretro
N13	N7	0.0192772	Saspease N14
N14	N13	0.0777208	Bel N15
N15	N14	0.0733086	TF N16
N16	N15	0.0642785	412_mdg1 Micropia_m
N17	N1	0.0036879	N18 N34
N18	N17	0.0512032	N19 N26
N19	N18	0.0571588	N20 N24
N20	N19	0.294803	Pep_a1_D2 N21
N21	N20	0.238258	Pep_a1_D1 N22
N22	N21	0.233599	Pep_a2_D1 N23
N23	N22	0.333776	Pep_a2_D2 Bs1
N24	N19	0.0614475	WdSV N25
N25	N24	0.0634049	Caulimovir Cer2-3
N26	N18	0.0320538	N27 N28
N27	N26	0.31056	DDI NIX
N28	N26	0.050986	Tat N29
N29	N28	0.0340162	Galadriel N30
N30	N29	0.0603139	N31 N32
N31	N30	0.144802	Mag Crm
N32	N30	0.02552	Del N33
N33	N32	0.17263	Reina Chrofung
N34	N17	0.0319906	N35 N36
N35	N34	0.196395	Errrativir COG5550
N36	N34	0.0921479	Gammaretro COG3577

Top

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	3.65493e-032	51	1.51072e-011	102	4.63421e-010	153	1.0697e-023
1	6.65984e-014	52	9.34627e-007	103	2.01722e-007	154	4.2154e-048
2	2.02521e-027	53	1.15796e-005	104	4.488e-005	155	9.98466e-054
3	1.27581e-009	54	8.42896e-005	105	0.000125535	156	1.216e-056
4	1.40669e-028	55	0.000116827	106	1.21104e-006	157	1.24239e-017
5	6.25812e-044	56	0.000688113	107	3.62287e-021	158	7.30604e-052
6	4.40742e-048	57	0.000656216	108	1.5613e-046	159	3.52599e-040
7	7.9856e-011	58	0.00268558	109	1.05276e-050	160	5.28405e-033
8	1.81313e-037	59	0.000214217	110	1.01429e-044	161	9.28402e-014
9	4.26962e-036	60	0.00230565	111	6.81398e-041	162	0.000140915
10	1.23471e-033	61	0.000116827	112	1.41915e-031	163	8.91109e-006
11	1.76312e-039	62	0.000116827	113	2.85131e-030	164	1.11702e-041
12	4.61622e-040	63	0.0017587	114	1.61621e-018	165	1.23438e-041
13	1.10944e-039	64	0.000412062	115	5.50661e-012	166	7.51892e-045
14	4.75167e-016	65	0.000191434	116	1.08495e-005	167	5.24702e-039
15	1.57694e-010	66	0.000191434	117	2.52956e-005	168	1.53912e-018
16	8.73126e-049	67	0.000191434	118	1.09106e-006	169	5.49698e-038
17	2.98116e-050	68	0.000486871	119	4.11897e-007	170	3.45828e-044
18	1.82889e-046	69	0.0017587	120	3.37139e-010	171	2.8636e-043
19	4.37751e-033	70	0.000183195	121	6.54006e-021	172	5.55407e-044
20	2.12295e-047	71	0.00245567	122	3.37784e-051	173	2.80835e-039
21	7.88518e-047	72	0.000214217	123	1.09371e-052	174	2.49615e-010
22	3.66793e-038	73	9.45288e-005	124	4.21498e-039	175	2.06994e-011
23	3.25065e-029	74	7.63583e-008	125	1.66493e-045	176	2.25184e-012
24	3.59626e-019	75	1.88683e-009	126	9.19282e-039	177	1.84654e-010
25	7.87687e-017	76	3.08692e-041	127	5.09933e-036	178	1.6356e-027
26	1.39816e-011	77	1.07506e-044	128	1.44995e-018	179	2.80774e-064
27	1.51648e-008	78	5.20035e-028	129	3.85828e-023	180	1.05922e-040
28	3.14563e-010	79	9.97212e-046	130	1.16693e-016	181	0.000148248
29	3.49738e-007	80	2.47447e-037	131	2.95596e-009	182	4.7975e-052
30	1.14011e-011	81	1.78502e-037	132	0.000146947	183	9.40954e-026
31	1.88164e-007	82	1.31147e-047	133	0.00473333	184	5.1773e-028
32	2.85738e-006	83	1.74972e-043	134	0.000462531	185	4.40087e-019
33	1.01795e-007	84	5.48791e-038	135	0.00473333	186	1.55817e-047
34	1.4126e-010	85	8.74907e-023	136	0.000160046	187	5.04219e-010
35	5.04079e-006	86	3.07178e-011	137	0.000381547	188	4.3761e-041
36	7.70125e-007	87	1.84268e-007	138	0.000462531	189	2.25635e-040
37	5.0019e-010	88	6.57823e-013	139	0.000160046	190	6.98505e-027
38	0.00476277	89	9.61228e-012	140	0.00040315	191	1.59518e-043
39	0.00122998	90	6.90353e-041	141	0.00193715	192	2.22451e-042
40	1.80499e-005	91	1.10753e-041	142	0.00473333	193	6.23918e-058
41	6.09371e-005	92	2.23453e-045	143	0.00193715	194	1.63186e-055
42	7.61903e-010	93	3.48495e-040	144	0.000146947	195	3.1242e-045
43	4.64531e-007	94	3.40288e-038	145	0.000143224	196	4.31858e-044
44	2.03959e-009	95	9.9027e-016	146	0.000381547	197	4.46853e-005
45	3.96775e-008	96	3.39815e-045	147	0.000525421	198	3.41362e-005
46	4.10678e-006	97	1.74049e-041	148	0.00473333	199	1.15611e-025
47	1.01618e-009	98	1.69803e-009	149	6.70045e-005	200	3.41384e-010
48	4.70471e-007	99	1.55646e-011	150	4.55345e-008	201	5.33898e-046
49	5.22036e-005	100	9.10951e-047	151	3.64186e-010	202	1.26589e-040
50	3.88565e-010	101	5.02402e-044	152	1.7055e-014	203	1.51263e-049
Total log likelihood of joint reconstruction:							-10065.8

Top

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="dtg_ilg_template" folder="jrof"></align>

Top

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	1.241e-029	51	3.0877e-009	102	1.88815e-008	153	8.5495e-022
1	7.42039e-014	52	0.000117762	103	4.7708e-005	154	1.00512e-045
2	2.24171e-026	53	0.000991631	104	0.00666005	155	1.50023e-049
3	1.28651e-009	54	0.00294804	105	0.00823224	156	4.3578e-053
4	4.0327e-027	55	0.068765	106	2.57812e-005	157	5.98468e-015
5	1.05345e-041	56	0.051691	107	5.70607e-019	158	8.42895e-050
6	4.25619e-046	57	0.051544	108	7.69038e-044	159	6.97358e-037
7	1.59099e-008	58	0.040126	109	1.33972e-048	160	1.03508e-030
8	4.61976e-036	59	0.058565	110	1.05365e-042	161	3.20305e-011
9	7.47296e-034	60	0.050901	111	1.49576e-038	162	0.022944
10	7.57821e-032	61	0.068765	112	2.08943e-029	163	0.00267218
11	1.40321e-037	62	0.068765	113	4.59726e-027	164	1.37445e-040
12	1.02102e-036	63	0.019803	114	1.82825e-016	165	5.98313e-039
13	1.06197e-036	64	0.076748	115	6.529e-010	166	5.5929e-042
14	1.66678e-014	65	0.042645	116	0.0041624	167	4.99776e-037
15	2.03815e-008	66	0.042645	117	0.00379727	168	9.30324e-016
16	4.30302e-045	67	0.042645	118	3.51582e-005	169	2.2717e-034
17	1.05581e-047	68	0.040752	119	7.54439e-006	170	3.1869e-042
18	1.09051e-043	69	0.019803	120	2.61863e-007	171	2.76975e-041
19	1.3733e-031	70	0.022944	121	1.65695e-018	172	2.68864e-040
20	6.69089e-045	71	0.032102	122	1.29344e-048	173	8.11278e-035
21	4.64629e-044	72	0.058565	123	1.1666e-049	174	1.66508e-008
22	1.08999e-035	73	0.00410718	124	8.35096e-037	175	4.40015e-009
23	4.40069e-026	74	4.11512e-005	125	2.22144e-043	176	6.10089e-010
24	1.27934e-016	75	2.60805e-007	126	3.45083e-037	177	1.40265e-007
25	2.89486e-014	76	1.25209e-037	127	1.10719e-033	178	7.81808e-025
26	7.99154e-010	77	1.30514e-041	128	1.37974e-015	179	6.96372e-060
27	3.1539e-006	78	3.8375e-027	129	2.05975e-022	180	5.86338e-038
28	6.04806e-008	79	2.22734e-041	130	2.53074e-014	181	0.068765
29	1.08898e-005	80	1.38449e-034	131	5.06178e-007	182	1.03544e-048
30	1.64407e-009	81	4.63485e-035	132	0.068765	183	9.66038e-025
31	5.21006e-006	82	6.33141e-045	133	0.091904	184	7.8082e-027
32	4.06059e-005	83	2.46188e-041	134	0.066005	185	5.00175e-019
33	4.10047e-005	84	1.62987e-034	135	0.091904	186	6.3561e-045
34	3.12234e-008	85	2.09587e-019	136	0.058565	187	2.56974e-008
35	0.000397755	86	8.68389e-009	137	0.040752	188	5.24888e-039
36	7.79889e-005	87	7.98166e-006	138	0.066005	189	1.30524e-038
37	2.16983e-007	88	1.95637e-010	139	0.058565	190	1.0888e-025
38	0.073152	89	1.27928e-009	140	0.076748	191	2.1615e-041
39	0.06183	90	9.19941e-038	141	0.050901	192	1.29921e-039
40	0.000120136	91	4.36078e-040	142	0.091904	193	3.35983e-054
41	0.0119932	92	2.38682e-042	143	0.050901	194	3.21372e-052
42	2.91172e-007	93	2.72772e-038	144	0.068765	195	1.16716e-042
43	6.07486e-005	94	4.16106e-037	145	0.042645	196	1.24378e-040
44	3.56275e-007	95	1.14424e-015	146	0.040752	197	0.0017366
45	1.55575e-006	96	9.76254e-042	147	0.051544	198	0.00140548
46	2.26002e-005	97	6.36682e-038	148	0.091904	199	2.42091e-022
47	1.07729e-007	98	8.35007e-007	149	0.00955424	200	8.31106e-008
48	1.3644e-005	99	1.7624e-008	150	5.07111e-006	201	2.81821e-043
49	0.00202625	100	9.41448e-044	151	1.43348e-007	202	1.09724e-039
50	1.2161e-007	101	2.25289e-041	152	1.66196e-011	203	2.26099e-046
Total log likelihood of joint reconstruction:							-9017.43

Top

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="dtg_ilg_template" folder="mrof"></align>

Top

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.

Top

HMMs

>AP_dtg_ilg_template profile HMM generated consensus sequence [hmmemit]
vDTGAsvsviskelaqklglsqPssktsttirgagGqskitsgqivtikitGnrslpsd
flvvtdpedydvILGrdfLrqlnsvidl

Top

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

Top

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.