CAARD:Pepsins A1b 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

(Nepheneshi:0.372257,NM_114992.:1.022165,(CND41_1:0.479291,(AtASP38_1:0.555408,Nucelin_1:0.620928)N3:0.048556)N2:0.043466);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Nepheneshi	N1	0.372257	-
NM_114992.	N1	1.02217	-
CND41_1	N2	0.479291	-
AtASP38_1	N3	0.555408	-
Nucelin_1	N3	0.620928	-
N1	root!	-	Nepheneshi NM_114992. N2
N2	N1	0.0434657	CND41_1 N3
N3	N2	0.0485564	AtASP38_1 Nucelin_1

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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	8.0937e-007	40	1.83718e-008	80	1.30364e-006	120	0.00141425
1	7.96508e-006	41	5.22093e-009	81	1.05024e-005	121	0.0102317
2	0.00256133	42	4.48241e-005	82	2.19433e-007	122	0.00339716
3	0.0011929	43	0.000404681	83	5.74433e-007	123	3.26869e-005
4	0.0102317	44	0.000866462	84	8.41431e-005	124	1.11534e-009
5	0.00107583	45	2.17095e-005	85	1.9603e-006	125	3.43243e-006
6	1.94063e-005	46	3.91443e-005	86	4.72459e-005	126	5.96334e-008
7	0.0127188	47	1.06869e-005	87	1.06673e-006	127	3.58198e-008
8	4.04918e-007	48	2.24262e-005	88	2.36328e-007	128	0.000193919
9	0.00535302	49	5.02363e-006	89	3.45778e-008	129	1.46051e-007
10	6.95352e-006	50	0.00339716	90	0.0001584	130	1.76118e-009
11	2.21254e-005	51	2.0962e-007	91	9.79644e-007	131	1.53111e-007
12	0.00339716	52	6.00608e-007	92	2.11605e-006	132	1.64533e-006
13	4.24714e-007	53	2.33951e-007	93	4.09457e-005	133	7.37841e-007
14	0.0211041	54	9.84382e-009	94	0.000377894	134	1.41788e-005
15	1.5393e-006	55	0.00339716	95	1.77281e-006	135	0.00157819
16	1.57468e-005	56	1.22688e-008	96	4.32346e-005	136	6.1302e-006
17	4.05652e-006	57	3.73132e-007	97	2.12379e-008	137	3.06715e-007
18	5.14417e-008	58	1.81482e-007	98	8.31931e-005	138	2.64686e-006
19	3.02574e-005	59	2.83274e-007	99	4.32465e-009	139	0.000233869
20	7.67795e-009	60	2.92569e-005	100	4.83222e-006	140	0.00100563
21	0.0182668	61	1.27261e-006	101	2.06245e-005	141	2.12538e-007
22	0.0185134	62	6.3242e-007	102	2.61833e-006	142	0.000233869
23	0.0463971	63	9.95861e-007	103	5.0156e-006	143	1.67091e-006
24	0.0236971	64	3.99297e-008	104	2.64804e-006	144	5.63293e-006
25	0.0244633	65	0.034129	105	9.12698e-006	145	1.96141e-007
26	0.0207248	66	0.000904001	106	5.88637e-007	146	0.00112721
27	0.0367895	67	2.55153e-007	107	8.8342e-007	147	2.79908e-007
28	0.0463971	68	6.07288e-007	108	0.000368383	148	7.12754e-005
29	0.0168121	69	4.13812e-005	109	0.00124509	149	4.63107e-005
30	0.0136403	70	8.21809e-009	110	2.39132e-005	150	5.89455e-005
31	1.55616e-005	71	0.0281867	111	1.56931e-007	151	8.33417e-007
32	1.13773e-005	72	0.034129	112	1.99203e-006	152	0.000169736
33	0.000119982	73	0.0509014	113	9.03888e-006	153	0.00031041
34	2.59878e-009	74	0.0509014	114	6.91843e-007	154	0.0015403
35	5.44181e-008	75	0.0509014	115	5.1244e-006	155	0.0138565
36	3.45672e-006	76	0.0509014	116	1.65247e-007	156	0.0138565
37	0.000111897	77	0.0509014	117	9.73438e-006
38	9.9788e-007	78	0.0509014	118	6.25912e-006
39	0.00552696	79	0.0509014	119	2.28911e-006
Total log likelihood of joint reconstruction:							-1698.83

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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_a1b_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	1.44819e-006	40	8.84727e-008	80	3.81103e-006	120	0.00141725
1	1.48728e-005	41	1.94639e-008	81	1.27706e-005	121	0.0102345
2	0.00257298	42	4.62054e-005	82	2.46344e-007	122	0.00339722
3	0.00119715	43	0.000450611	83	6.30665e-007	123	3.28885e-005
4	0.0102345	44	0.000902559	84	8.41818e-005	124	3.91382e-009
5	0.00108226	45	2.52308e-005	85	3.05718e-006	125	4.83463e-006
6	2.24004e-005	46	5.47497e-005	86	4.74605e-005	126	8.87774e-008
7	0.0127329	47	3.57707e-005	87	1.63538e-006	127	1.15113e-007
8	6.68257e-007	48	4.57591e-005	88	3.41268e-007	128	0.000195067
9	0.00535303	49	5.07502e-006	89	1.35614e-007	129	3.7541e-007
10	8.78311e-006	50	0.00339722	90	0.000158647	130	7.10525e-009
11	2.2503e-005	51	7.36257e-007	91	1.83686e-006	131	1.98691e-007
12	0.00339722	52	9.29883e-007	92	2.17329e-006	132	2.10034e-006
13	9.07418e-007	53	2.69018e-007	93	4.17917e-005	133	2.15888e-006
14	0.032102	54	2.19084e-008	94	0.000384071	134	6.17061e-005
15	1.55537e-006	55	0.00339722	95	2.67291e-006	135	0.00205962
16	1.57867e-005	56	2.06831e-008	96	7.1603e-005	136	2.76055e-005
17	6.10247e-006	57	5.41705e-007	97	3.31862e-008	137	4.68006e-007
18	8.20032e-008	58	2.97737e-007	98	8.34521e-005	138	3.96523e-006
19	3.03171e-005	59	9.86034e-007	99	7.9424e-009	139	0.000234571
20	2.99516e-008	60	4.23627e-005	100	6.13905e-006	140	0.00101938
21	0.051691	61	2.32953e-006	101	2.2375e-005	141	1.15528e-006
22	0.051544	62	3.56516e-006	102	3.8739e-006	142	0.000234571
23	0.091904	63	3.09907e-006	103	1.00313e-005	143	2.12989e-006
24	0.058676	64	4.07409e-007	104	3.01664e-006	144	5.71771e-006
25	0.06183	65	0.066005	105	9.29703e-006	145	2.0461e-007
26	0.066005	66	0.000905927	106	1.02901e-006	146	0.00113441
27	0.073152	67	4.87752e-007	107	1.37986e-006	147	6.56039e-007
28	0.091904	68	7.48004e-007	108	0.0011114	148	7.95396e-005
29	0.068765	69	4.1521e-005	109	0.00364993	149	6.35825e-005
30	0.040752	70	2.396e-008	110	2.45418e-005	150	6.3369e-005
31	2.67965e-005	71	0.058565	111	3.16862e-007	151	4.61356e-006
32	1.35652e-005	72	0.066005	112	2.85513e-006	152	0.000178385
33	0.000120108	73	0.073152	113	1.80595e-005	153	0.000312563
34	8.81003e-009	74	0.073152	114	1.33902e-006	154	0.0017739
35	1.28789e-007	75	0.073152	115	2.81094e-005	155	1
36	3.89873e-006	76	0.073152	116	4.17211e-007	156	1
37	0.000118442	77	0.073152	117	1.03608e-005
38	1.92756e-006	78	0.073152	118	7.18212e-006
39	0.00552829	79	0.073152	119	4.26786e-006
Total log likelihood of joint reconstruction:							-1614.21

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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_a1b_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_a1b_d1 profile HMM generated consensus sequence
iiDTGSDLtWLqCnpCSnCnsqPtpLFdPngSssYStvpCssqrCqdlsrdftPssCan
nnqChYtlsYgdGSsSqGvLatdtftfGnssvdsNIaFGCGennrGfnqgnptptaGLl
Gmgrgslslpsql

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

        Domain 1 of 1, from 2 to 131: score 34.6, E = 3.7e-11

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkk.a.fdp..SS.Y..v.C...
                    +DTG++++++   +c + +   +++++++ fdp++SS+Y++v+C+++
AP_pepsins     2    IDTGSDLTWL---QC-NPC-SNCNSQPtPlFDPngSSsYstVpCssq 43   

                 ivt.l..................lsysqPssktsttaqdtirgagGqski
                 ++++l+++ ++++  ++++ + +lsy+++ss ++++a+dt+ ++g+    
AP_pepsins    44 RCQdLsrdftpsscannnqchytLSYGDGSSSQGVLATDTF-TFGN---- 88   

                 yvSklktsgqirknllslvtikitkGnvTevenrslpsdgvflvvtdped
                       +s+          +++ + G       + +   g f +  +p  
AP_pepsins    89 ------SSV---------DSNIAF-G-------CGENNRG-FNQG-NPTP 113  

                 qksrydvILGrldfLrqlnsvhidl<-*
                       ++LG+ ++ +   +   +l   
AP_pepsins   114 ----TAGLLGM-GRGSLSLP--SQL    131  

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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.