CAARD:Pepsins A1a d2

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

((CatDchi2:0.124412,CatDonc2:0.082390)N2:0.053454,(CatDceg2:0.248584,(NapAmo2:0.368014,((CatDdro2:0.191392,CatDschi2:0.321620) N6:0.074849,(((Renrat2:0.220135,Rencal2:0.227798)N9:0.224064,(Eimpeim2:0.451561,Plasmep1pl:0.675691)N10:0.047604)N8:0.085498, ((Sccpepcan2:0.426127,(Gastmac2:0.427370,(Mucorhi2:0.784918,((SAP7can2:0.674817,Cparapcan2:0.609072)N16:0.193456, ((Memapsin1h:0.347342,Memapsin2h:0.251921)N18:0.495260,(Sypepsyn2:0.560354,(Enpepcry2:0.352425,Ppeppen2:0.254676)N20:0.205481) N19:0.158248)N17:0.068820)N15:0.012393)N14:0.116440)N13:0.028146)N12:0.089438,(CatExen2:0.270432,(PepArin2:0.227019, (Pepgal2:0.337171,PepFequ2:0.414174)N23:0.021412)N22:0.070832)N21:0.044379)N11:0.027323)N7:0.061125)N5:0.043160)N4:0.007450) N3:0.032229,(CatDgal2:0.208863,(CatDhum2:0.146380,CatDhyn2:0.119802)N25:0.028346)N24:0.007137);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
CatDchi2	N2	0.124412	-
CatDonc2	N2	0.0823897	-
CatDceg2	N3	0.248584	-
NapAmo2	N4	0.368014	-
CatDdro2	N6	0.191392	-
CatDschi2	N6	0.32162	-
Renrat2	N9	0.220135	-
Rencal2	N9	0.227798	-
Eimpeim2	N10	0.451561	-
Plasmep1pl	N10	0.675691	-
Sccpepcan2	N12	0.426127	-
Gastmac2	N13	0.42737	-
Mucorhi2	N14	0.784918	-
SAP7can2	N16	0.674817	-
Cparapcan2	N16	0.609072	-
Memapsin1h	N18	0.347342	-
Memapsin2h	N18	0.251921	-
Sypepsyn2	N19	0.560354	-
Enpepcry2	N20	0.352425	-
Ppeppen2	N20	0.254676	-
CatExen2	N21	0.270432	-
PepArin2	N22	0.227019	-
Pepgal2	N23	0.337171	-
PepFequ2	N23	0.414174	-
CatDgal2	N24	0.208863	-
CatDhum2	N25	0.14638	-
CatDhyn2	N25	0.119802	-
N1	root!	-	N2 N3 N24
N2	N1	0.0534545	CatDchi2 CatDonc2
N3	N1	0.0322288	CatDceg2 N4
N4	N3	0.00745046	NapAmo2 N5
N5	N4	0.0431602	N6 N7
N6	N5	0.0748491	CatDdro2 CatDschi2
N7	N5	0.0611249	N8 N11
N8	N7	0.0854978	N9 N10
N9	N8	0.224064	Renrat2 Rencal2
N10	N8	0.0476035	Eimpeim2 Plasmep1pl
N11	N7	0.0273227	N12 N21
N12	N11	0.0894381	Sccpepcan2 N13
N13	N12	0.028146	Gastmac2 N14
N14	N13	0.11644	Mucorhi2 N15
N15	N14	0.0123925	N16 N17
N16	N15	0.193456	SAP7can2 Cparapcan2
N17	N15	0.0688203	N18 N19
N18	N17	0.49526	Memapsin1h Memapsin2h
N19	N17	0.158248	Sypepsyn2 N20
N20	N19	0.205481	Enpepcry2 Ppeppen2
N21	N11	0.0443787	CatExen2 N22
N22	N21	0.0708323	PepArin2 N23
N23	N22	0.021412	Pepgal2 PepFequ2
N24	N1	0.00713701	CatDgal2 N25
N25	N24	0.0283457	CatDhum2 CatDhyn2

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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	4.94094e-017	37	4.31185e-005	74	3.51464e-035	111	5.33244e-016
1	5.57941e-007	38	0.000120145	75	1.13017e-044	112	2.75464e-010
2	8.38563e-012	39	1.06592e-016	76	1.63349e-024	113	3.30375e-033
3	4.85499e-005	40	9.80352e-028	77	4.58615e-030	114	2.87831e-027
4	3.1369e-010	41	2.93883e-017	78	2.05358e-005	115	1.33256e-021
5	5.07064e-011	42	1.15015e-031	79	1.37119e-015	116	6.8233e-011
6	4.62614e-018	43	2.60512e-018	80	2.56005e-022	117	0.0013376
7	8.04008e-018	44	2.00401e-032	81	2.44994e-027	118	3.50171e-006
8	1.60938e-028	45	3.0187e-005	82	2.2556e-034	119	7.00563e-019
9	8.32192e-016	46	1.75929e-026	83	4.4112e-031	120	4.6136e-025
10	1.6694e-012	47	3.16716e-005	84	6.37787e-012	121	5.21357e-021
11	5.70622e-035	48	2.12209e-005	85	0.00064118	122	7.36872e-013
12	3.69498e-032	49	0.000557609	86	2.26245e-025	123	1.39168e-012
13	1.18278e-029	50	3.02287e-005	87	1.04723e-028	124	4.85499e-005
14	5.21348e-023	51	0.000168844	88	3.68479e-023	125	0.00306766
15	0.000372035	52	1.90925e-032	89	1.13955e-034	126	6.25802e-013
16	2.17025e-011	53	4.10285e-030	90	3.48358e-022	127	1.33452e-020
17	2.63053e-039	54	9.49964e-028	91	1.09003e-010	128	1.13531e-010
18	2.46171e-035	55	1.61502e-030	92	3.99096e-013	129	1.10816e-017
19	5.34598e-029	56	2.5761e-016	93	3.19415e-020	130	2.3978e-014
20	2.09935e-026	57	1.13087e-007	94	6.13553e-040	131	4.70512e-031
21	3.60249e-032	58	6.16256e-005	95	9.94857e-014	132	2.63348e-017
22	0.0003113	59	8.61014e-010	96	1.42392e-024	133	1.49577e-013
23	2.13297e-030	60	7.12792e-037	97	1.91691e-020	134	1.04752e-019
24	5.72777e-016	61	7.323e-021	98	4.54469e-028	135	2.0358e-016
25	4.4986e-015	62	2.33191e-026	99	3.0187e-005	136	2.39004e-009
26	1.86447e-013	63	6.04569e-017	100	3.32302e-025	137	6.84931e-010
27	5.62491e-005	64	2.44523e-039	101	1.59141e-014	138	0.0142937
28	0.000105914	65	2.7881e-025	102	2.16154e-012	139	9.47552e-025
29	7.82516e-013	66	1.57491e-023	103	2.4206e-016	140	6.0131e-028
30	1.68331e-037	67	1.69989e-009	104	1.0509e-030	141	1.56861e-026
31	5.36881e-027	68	1.84721e-005	105	7.44251e-021	142	3.18695e-022
32	2.78921e-027	69	6.2142e-009	106	1.12762e-022	143	5.13349e-025
33	8.26258e-034	70	1.69934e-006	107	3.46639e-012	144	7.15639e-013
34	4.63722e-030	71	1.69862e-005	108	1.08623e-006	145	6.7068e-009
35	5.85682e-006	72	1.04907e-007	109	1.45573e-005	146	1.55118e-013
36	3.13127e-005	73	1.00911e-007	110	8.21575e-024
Total log likelihood of joint reconstruction:							-5979.9

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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_d2" 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	1.43403e-016	37	0.000209369	74	1.66248e-033	111	2.55966e-015
1	5.69315e-007	38	0.0011179	75	2.15894e-042	112	5.86543e-009
2	1.01213e-011	39	5.273e-016	76	1.27158e-023	113	6.3741e-032
3	4.86247e-005	40	1.0718e-025	77	1.05031e-029	114	9.42056e-027
4	3.52034e-010	41	7.42972e-017	78	0.000486728	115	2.596e-020
5	7.13239e-011	42	2.93695e-031	79	4.61461e-015	116	4.6494e-010
6	5.62984e-018	43	1.37577e-017	80	1.1481e-021	117	0.0307901
7	1.13039e-016	44	2.52127e-031	81	7.60626e-026	118	0.000120002
8	5.3983e-027	45	3.01897e-005	82	1.21371e-032	119	7.5057e-018
9	1.07048e-015	46	3.026e-026	83	2.78912e-029	120	1.29241e-023
10	2.26856e-012	47	0.000652008	84	1.3444e-011	121	2.66532e-020
11	3.87047e-033	48	0.00130118	85	0.00479164	122	1.60138e-012
12	2.90212e-031	49	0.00387182	86	7.19269e-024	123	4.63714e-012
13	2.02869e-028	50	0.000773129	87	5.70947e-028	124	4.86247e-005
14	5.82542e-022	51	0.00315376	88	2.17718e-022	125	0.051544
15	0.068765	52	9.97463e-030	89	2.38317e-033	126	7.62804e-013
16	1.46816e-009	53	1.19872e-028	90	2.36317e-021	127	1.00179e-019
17	1.20194e-037	54	5.06038e-027	91	1.91207e-009	128	1.94684e-010
18	4.52193e-033	55	3.39022e-029	92	2.28514e-011	129	1.83492e-017
19	9.06587e-028	56	3.46636e-016	93	9.53966e-019	130	5.55369e-014
20	2.71969e-025	57	6.74451e-006	94	8.78935e-038	131	4.36333e-030
21	5.57062e-031	58	0.000711655	95	2.95601e-013	132	2.52605e-016
22	0.00780915	59	1.13836e-009	96	4.52399e-023	133	1.87238e-013
23	3.47568e-029	60	2.30963e-034	97	5.83155e-019	134	9.8498e-019
24	2.01026e-014	61	4.70893e-020	98	4.71229e-027	135	3.48592e-016
25	1.22459e-014	62	1.62484e-025	99	3.01897e-005	136	4.35359e-009
26	2.68186e-013	63	1.13445e-016	100	1.2267e-023	137	9.26567e-010
27	0.00110595	64	1.20312e-037	101	2.40957e-013	138	0.073152
28	0.000351207	65	1.2696e-024	102	1.27481e-011	139	8.19025e-024
29	2.73261e-011	66	3.06999e-022	103	1.05068e-015	140	7.5968e-027
30	3.75556e-036	67	2.07178e-009	104	2.42764e-029	141	3.38358e-025
31	2.22656e-025	68	0.000535229	105	1.33533e-019	142	6.15789e-022
32	2.10844e-026	69	3.86228e-007	106	2.77548e-021	143	5.17223e-024
33	8.973e-032	70	5.46968e-005	107	3.49388e-011	144	4.99939e-012
34	1.19482e-028	71	0.000633539	108	0.000133871	145	1.17126e-008
35	5.48105e-005	72	1.03907e-006	109	0.000437352	146	2.55118e-013
36	0.000343088	73	1.43079e-006	110	1.83318e-023
Total log likelihood of joint reconstruction:							-5641.19

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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_d2" 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_d2 profile HMM generated consensus sequence
vDTGTSLitgPssvvqalqkaiGAtessdgeYvvnCskintLPtitFtlgGkqytLpps
dYvlqvsGiClsGfggmDipplwILGDvFlrkyYtVFDrdnnrVGF

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

         Domain 1 of 1, from 1 to 98: score 40.9, E = 4.8e-13

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdp..SS...Y.v.C..iv
                    vDTG+s+++ +s  + +a++++      +++++SS+++Y v+C++i+
AP_pepsins     1    VDTGTSLITGPSSVV-QALQKA------IGAteSSdgeYvVnCskIN 40   

                 tllsysqPssktsttaqdtirgagGqskiyvSklktsgqirknllslvti
                      ++P+  ++      + + gG  k+y    + +++       ++ +
AP_pepsins    41 -----TLPT--IT------F-TLGG--KQY----TLPPS-------DYVL 63   

                 kitkGnvTevenrslpsdgvflvv.tdpedqksrydvILGrldfLrqlns
                 ++  G       +  +    f    ++p      + +ILG+  fLr++++
AP_pepsins    64 QVS-G------ICLSG----F-GGmDIP------PLWILGD-VFLRKYYT 94   

                 vhidl<-*
                 v +d+   
AP_pepsins    95 V-FDR    98   

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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.