CAARD:Pepsins A1a d1

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

((Plasmepsin:0.619584,((Mucorhi1:0.588375,Eimpeim1:0.453746)N4:0.071315,((Sypepsyn1:0.330143,(Ppeppen1:0.259579,Enpepcry1:0.237607) N7:0.229824)N6:0.135018,((Memapsin1h:0.315785,Memapsin2h:0.249853)N9:0.402007,(Cparapcan1:0.435582,SAP7can1:0.508581)N10:0.163198) N8:0.054444)N5:0.032440)N3:0.055109)N2:0.058724,((CatDdro1:0.207070,Sccpepcan1:0.326066)N12:0.032808,(CatDceg1:0.338483, (CatDschi1:0.205753,(CatDgal1:0.133100,(CatDhum1:0.267800,(CatDhyn1:0.103214,(CatDonc1:0.039951,CatDchi1:0.050869)N18:0.062134) N17:0.020139)N16:0.012072)N15:0.074766)N14:0.020364)N13:0.023514)N11:0.044815,((CatExen1:0.226556,(Gastmac1:0.308945, (Pepgal1:0.218648,(PepFequ1:0.295050,PepArin1:0.210448)N23:0.037629)N22:0.033798)N21:0.029503)N20:0.111089,(NapAmo1:0.298268, (Renrat1:0.178563,Rencal1:0.219815)N25:0.204093)N24:0.024229)N19:0.006440);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Plasmepsin	N2	0.619584	-
Mucorhi1	N4	0.588375	-
Eimpeim1	N4	0.453746	-
Sypepsyn1	N6	0.330143	-
Ppeppen1	N7	0.259579	-
Enpepcry1	N7	0.237607	-
Memapsin1h	N9	0.315785	-
Memapsin2h	N9	0.249853	-
Cparapcan1	N10	0.435582	-
SAP7can1	N10	0.508581	-
CatDdro1	N12	0.20707	-
Sccpepcan1	N12	0.326066	-
CatDceg1	N13	0.338483	-
CatDschi1	N14	0.205753	-
CatDgal1	N15	0.1331	-
CatDhum1	N16	0.2678	-
CatDhyn1	N17	0.103214	-
CatDonc1	N18	0.0399508	-
CatDchi1	N18	0.0508695	-
CatExen1	N20	0.226556	-
Gastmac1	N21	0.308945	-
Pepgal1	N22	0.218648	-
PepFequ1	N23	0.29505	-
PepArin1	N23	0.210448	-
NapAmo1	N24	0.298268	-
Renrat1	N25	0.178563	-
Rencal1	N25	0.219815	-
N1	root!	-	N2 N11 N19
N2	N1	0.0587244	Plasmepsin N3
N3	N2	0.0551087	N4 N5
N4	N3	0.0713151	Mucorhi1 Eimpeim1
N5	N3	0.03244	N6 N8
N6	N5	0.135018	Sypepsyn1 N7
N7	N6	0.229824	Ppeppen1 Enpepcry1
N8	N5	0.0544444	N9 N10
N9	N8	0.402007	Memapsin1h Memapsin2h
N10	N8	0.163198	Cparapcan1 SAP7can1
N11	N1	0.0448152	N12 N13
N12	N11	0.0328084	CatDdro1 Sccpepcan1
N13	N11	0.0235138	CatDceg1 N14
N14	N13	0.020364	CatDschi1 N15
N15	N14	0.0747663	CatDgal1 N16
N16	N15	0.0120716	CatDhum1 N17
N17	N16	0.0201385	CatDhyn1 N18
N18	N17	0.062134	CatDonc1 CatDchi1
N19	N1	0.00643973	N20 N24
N20	N19	0.111089	CatExen1 N21
N21	N20	0.0295032	Gastmac1 N22
N22	N21	0.0337978	Pepgal1 N23
N23	N22	0.0376293	PepFequ1 PepArin1
N24	N19	0.0242294	NapAmo1 N25
N25	N24	0.204093	Renrat1 Rencal1

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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	1.57781e-009	43	3.81446e-039	86	0.00517803	129	3.12784e-013
1	3.50414e-006	44	1.73779e-023	87	0.0215351	130	0.00263569
2	2.48179e-007	45	4.53685e-007	88	1.70663e-022	131	0.00241536
3	0.000163858	46	0.000132969	89	1.25428e-019	132	3.92194e-007
4	1.11117e-007	47	0.0191658	90	2.57776e-023	133	0.00699781
5	1.06101e-011	48	0.00257837	91	5.26452e-042	134	5.27849e-024
6	1.16e-011	49	5.93795e-011	92	7.29433e-024	135	9.3712e-031
7	1.56882e-010	50	1.92363e-025	93	0.000240074	136	1.42885e-009
8	1.83393e-006	51	3.02305e-031	94	2.56137e-037	137	1.75103e-023
9	3.57934e-011	52	0.00418673	95	5.15622e-032	138	2.27454e-021
10	9.34664e-015	53	0.00379987	96	7.35543e-014	139	3.5293e-011
11	1.82275e-011	54	5.33712e-022	97	1.57836e-036	140	2.28218e-006
12	0.00121012	55	5.37481e-029	98	1.09138e-011	141	1.29124e-005
13	0.000209351	56	2.57533e-014	99	6.13381e-017	142	7.76068e-023
14	0.00196933	57	6.11189e-031	100	2.2621e-014	143	5.03096e-035
15	2.24754e-025	58	0.000107549	101	3.93064e-018	144	1.23292e-029
16	1.85793e-025	59	2.73109e-012	102	3.42667e-031	145	2.64246e-021
17	6.01532e-009	60	1.7434e-019	103	0.000138263	146	3.82402e-028
18	0.000275473	61	0.000163858	104	7.78449e-033	147	9.59371e-011
19	0.00359027	62	3.07528e-021	105	5.61524e-022	148	7.76025e-006
20	1.52583e-017	63	1.54296e-006	106	5.48253e-014	149	5.84296e-005
21	2.22854e-020	64	1.10097e-021	107	1.33023e-021	150	1.9744e-014
22	2.89413e-032	65	2.56224e-025	108	2.81822e-031	151	1.2577e-028
23	1.15099e-021	66	2.69949e-006	109	1.14296e-029	152	1.23442e-018
24	8.77868e-025	67	8.72986e-032	110	6.15328e-012	153	1.24454e-019
25	1.46125e-017	68	2.86576e-027	111	3.14941e-029	154	6.5831e-025
26	0.0109094	69	0.00144514	112	6.27328e-010	155	1.78284e-024
27	2.61775e-009	70	2.17415e-019	113	0.00303256	156	5.19879e-033
28	2.04772e-039	71	1.43954e-028	114	0.00199313	157	2.42067e-032
29	2.11629e-033	72	3.50414e-006	115	0.00826312	158	1.88211e-015
30	9.77622e-017	73	3.31617e-023	116	0.00179456	159	3.07712e-023
31	2.18054e-031	74	9.53364e-018	117	0.000324837	160	7.91072e-026
32	2.36159e-027	75	5.20412e-026	118	2.66695e-025	161	1.93661e-025
33	4.65787e-012	76	9.48168e-019	119	2.74398e-019	162	1.36541e-029
34	6.66723e-021	77	0.000374123	120	1.03705e-028	163	5.90665e-033
35	1.07017e-023	78	0.00569751	121	3.77463e-015	164	3.88203e-029
36	3.04273e-031	79	0.00416667	122	8.07189e-010	165	1.67091e-021
37	3.275e-031	80	0.00301618	123	0.000163858	166	1.77373e-007
38	1.11117e-007	81	0.00517803	124	4.36959e-011	167	1.70787e-016
39	1.6086e-014	82	0.00301618	125	1.95391e-012	168	9.4127e-021
40	8.98171e-011	83	0.00301618	126	0.000163858	169	1.50813e-018
41	2.91712e-015	84	0.00517803	127	2.61029e-013	170	1.63551e-015
42	7.52062e-028	85	0.00301618	128	3.66987e-017
Total log likelihood of joint reconstruction:							-6213.39

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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="pepsins_a1a_d1" 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	3.34251e-009	43	3.05371e-037	86	0.076748	129	5.75976e-013
1	3.54939e-006	44	2.42892e-022	87	0.091904	130	0.058565
2	2.50684e-007	45	3.49699e-006	88	1.36361e-021	131	0.068765
3	0.00016402	46	0.00229331	89	2.50311e-019	132	2.8083e-006
4	1.12845e-007	47	0.091904	90	5.49643e-022	133	0.06183
5	1.2665e-011	48	0.058565	91	3.32244e-040	134	2.90441e-022
6	3.62428e-011	49	6.10382e-011	92	5.33894e-023	135	1.09448e-029
7	2.37112e-010	50	5.83566e-024	93	0.00582599	136	1.16641e-008
8	1.92388e-006	51	8.33377e-030	94	8.95451e-037	137	2.22109e-022
9	3.94487e-011	52	0.076748	95	5.03291e-031	138	2.87431e-020
10	1.90098e-013	53	0.066005	96	1.16863e-013	139	4.46269e-010
11	4.00658e-011	54	1.02315e-021	97	1.69357e-035	140	4.30976e-005
12	0.0208031	55	5.71144e-028	98	1.59169e-011	141	0.000243769
13	0.00189978	56	6.90962e-014	99	3.46818e-016	142	1.40991e-021
14	0.042645	57	2.8051e-029	100	3.63896e-013	143	3.48369e-033
15	1.09625e-024	58	0.000107696	101	7.38059e-018	144	2.43725e-028
16	1.82739e-024	59	3.10544e-012	102	9.52361e-030	145	1.0427e-020
17	2.75977e-008	60	4.32435e-019	103	0.0017831	146	1.50499e-027
18	0.00308764	61	0.00016402	104	2.64125e-031	147	5.89056e-010
19	0.066005	62	1.05825e-020	105	3.26134e-021	148	0.000126302
20	7.08355e-016	63	3.13799e-005	106	1.1691e-013	149	0.000939208
21	8.27968e-019	64	4.58474e-021	107	1.2043e-020	150	5.64029e-014
22	6.69124e-031	65	9.41842e-025	108	3.9134e-030	151	3.93207e-028
23	6.81495e-021	66	2.72295e-006	109	3.90017e-028	152	1.44839e-018
24	4.4163e-024	67	3.14928e-030	110	1.15676e-011	153	1.58141e-019
25	4.42521e-016	68	2.34229e-026	111	4.03159e-028	154	2.88988e-024
26	0.0385965	69	0.023826	112	2.65099e-008	155	1.4066e-023
27	8.10582e-009	70	8.86579e-019	113	0.040752	156	2.7059e-032
28	1.76359e-037	71	6.60123e-028	114	0.068765	157	1.31139e-031
29	3.22736e-032	72	3.54939e-006	115	0.050901	158	2.18749e-015
30	1.57764e-016	73	5.48229e-023	116	0.042645	159	1.33166e-022
31	5.87258e-030	74	1.28698e-017	117	0.00777343	160	1.92666e-025
32	3.10825e-026	75	2.20247e-025	118	1.55377e-024	161	5.66728e-024
33	6.37907e-012	76	3.92732e-018	119	8.25521e-018	162	8.35743e-029
34	1.70946e-020	77	0.00109304	120	3.33439e-027	163	3.17694e-032
35	1.4559e-022	78	0.019803	121	1.11701e-014	164	3.34513e-028
36	1.98059e-030	79	0.040752	122	2.25426e-009	165	1.2324e-020
37	1.86749e-030	80	0.068765	123	0.00016402	166	2.24069e-007
38	1.12845e-007	81	0.076748	124	1.12148e-010	167	6.17886e-016
39	4.48316e-014	82	0.068765	125	2.32044e-012	168	2.54455e-020
40	3.00031e-010	83	0.068765	126	0.00016402	169	3.46674e-018
41	1.26268e-014	84	0.076748	127	7.97693e-013	170	2.87298e-015
42	1.34742e-027	85	0.068765	128	1.39808e-016
Total log likelihood of joint reconstruction:							-5892.98

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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="pepsins_a1a_d1" 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_pepsins_a1a_d1 profile HMM generated consensus sequence
FDTGSSNLWVpStqChgtsiaCslhnkFdpskSSTYkenGtfsIqYGtGsslsGflsqD
tVtigGltvtnqtfgeavkepgstFvdakfDGILGLgYpslavdgvtpvfdnlikqgli
ekpvFSvyL

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

        Domain 1 of 1, from 1 to 104: score 45.8, E = 1.6e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkk.a.fdp..SS.Y..v.C.iv
                    +DTG+s l+v+s++c +    +++  ++++fdp++SS+Y+++++ ++
AP_pepsins     1    FDTGSSNLWVPSTQC-HGTSIACS--LhNkFDPskSStYkeNgTfSI 44   

                 tllsysqPssktsttaqdtirgagGqskiyvSklktsgqirknllslvti
                 +   y+ +ss  + ++qdt+ ++gG   +                  vt+
AP_pepsins    45 Q---YGTGSSLSGFLSQDTV-TIGG--LT------------------VTN 70   

                 kitkGnvTevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsv
                 +++ G++    +++++s+  f+++        ++d+ILG+ +  + +   
AP_pepsins    71 QTF-GEA----VKEPGST--FVDA--------KFDGILGL-GYPSLA--- 101  

                 hidl<-*
                  +d    
AP_pepsins   102 -VDG    104  

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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.