CAARD:Pepsins A1b 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

(Nepheneshi:0.598438,Nucelin_2:1.004286,(CND41_2:0.590814,(AtASP38_2:0.777249,NM_114992.:0.693684)N3:0.138354)N2:0.127675);

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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	0.598438	-
Nucelin_1	N1	1.00429	-
CND41_1	N2	0.590814	-
AtASP38_1	N3	0.777249	-
NM_114992.	N3	0.693684	-
N1	root!	-	Nepheneshi Nucelin_2 N2
N2	N1	0.127675	CND41_2 N3
N3	N2	0.138354	AtASP38_2 NM_114992.

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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	1.05584e-008	38	1.23182e-006	76	0.000659766	114	9.39552e-009
1	8.77643e-007	39	2.93795e-008	77	1.46946e-007	115	1.81676e-006
2	3.75738e-006	40	1.99776e-008	78	5.63291e-009	116	1.43145e-008
3	7.47592e-007	41	3.0526e-007	79	2.3127e-008	117	1.27613e-007
4	0.00123823	42	3.64986e-008	80	6.88547e-008	118	1.49639e-006
5	8.98428e-005	43	1.91231e-007	81	4.78394e-008	119	1.14191e-005
6	0.00628563	44	1.06537e-006	82	3.67134e-008	120	0.00938721
7	0.000202103	45	1.75269e-006	83	3.21952e-007	121	0.000110466
8	3.34591e-007	46	3.65546e-005	84	1.09494e-007	122	2.26106e-005
9	2.92737e-006	47	1.12667e-006	85	1.43234e-005	123	0.00628563
10	0.000462267	48	5.72498e-008	86	2.00736e-005	124	2.1602e-007
11	4.63047e-007	49	0.00218568	87	0.000154799	125	6.98604e-009
12	0.000821593	50	5.62517e-006	88	0.000393045	126	3.74952e-008
13	6.93083e-007	51	8.3167e-008	89	0.000160279	127	2.01219e-007
14	3.2791e-008	52	3.6746e-007	90	2.63554e-005	128	4.80926e-007
15	2.34297e-007	53	0.000190547	91	4.41311e-007	129	5.88745e-007
16	1.91937e-007	54	0.000285897	92	1.30181e-005	130	1.03307e-009
17	0.00324838	55	0.0205774	93	1.56149e-006	131	4.10085e-008
18	1.78577e-008	56	0.00352966	94	2.37157e-009	132	0.000122005
19	4.22659e-005	57	0.00742295	95	3.89863e-008	133	2.31701e-006
20	8.76524e-006	58	1.5757e-006	96	0.000120063	134	9.19051e-005
21	1.39693e-007	59	7.60743e-008	97	0.000987447	135	0.00123823
22	1.10047e-007	60	9.02912e-007	98	0.000529163	136	1.18171e-007
23	1.46188e-007	61	7.06964e-008	99	0.000535224	137	4.69255e-007
24	0.000226527	62	6.43748e-008	100	0.00235461	138	2.30455e-006
25	3.05265e-008	63	9.50906e-008	101	3.76736e-009	139	3.45341e-007
26	2.67186e-007	64	7.60476e-008	102	5.32088e-007	140	5.27395e-008
27	7.98697e-007	65	3.11385e-008	103	0.00218568	141	6.02463e-005
28	4.40938e-007	66	6.65053e-007	104	0.0417853	142	0.00048424
29	1.09657e-006	67	0.000174205	105	0.0332422	143	2.84862e-008
30	0.0379915	68	8.70328e-009	106	8.19313e-005	144	8.23376e-007
31	0.000208277	69	1.11598e-005	107	4.27604e-005	145	3.45384e-008
32	0.000405029	70	1.89745e-005	108	6.622e-007	146	9.42145e-009
33	0.000198936	71	1.40409e-005	109	0.00050124	147	1.65115e-006
34	1.77253e-008	72	4.13386e-008	110	2.9649e-006	148	0.00218568
35	2.70619e-010	73	0.00049691	111	1.45167e-007
36	1.24788e-007	74	5.05574e-005	112	8.36337e-008
37	3.67762e-010	75	0.000500941	113	4.64907e-009
Total log likelihood of joint reconstruction:							-1911.36

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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_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	7.0606e-008	38	3.88275e-006	76	0.000671543	114	7.50107e-008
1	2.44515e-006	39	1.34277e-007	77	3.45572e-007	115	3.67835e-006
2	1.69595e-005	40	5.0922e-008	78	1.71745e-008	116	9.59926e-008
3	1.71535e-006	41	5.12374e-007	79	6.39184e-008	117	7.6041e-007
4	0.00126388	42	2.59235e-007	80	2.77404e-007	118	4.44491e-006
5	0.000102883	43	5.39239e-007	81	2.8946e-007	119	3.80404e-005
6	0.00629391	44	1.51615e-006	82	1.43325e-007	120	0.042645
7	0.00021335	45	6.63099e-006	83	4.51384e-007	121	0.000135864
8	6.70594e-007	46	4.15319e-005	84	5.20175e-007	122	2.56221e-005
9	3.45917e-006	47	3.24688e-006	85	6.10889e-005	123	0.00629391
10	0.000470541	48	4.19103e-007	86	0.000112138	124	5.41333e-007
11	6.11003e-007	49	0.00218583	87	0.000678693	125	4.10995e-008
12	0.000844953	50	6.88316e-006	88	0.00177444	126	9.07419e-008
13	3.02291e-006	51	2.98002e-007	89	0.000946008	127	2.11889e-007
14	1.01845e-007	52	1.94885e-006	90	2.87983e-005	128	5.96466e-007
15	5.94928e-007	53	0.000461756	91	7.69054e-007	129	2.3831e-006
16	6.35624e-007	54	0.00131249	92	1.86208e-005	130	6.10716e-009
17	0.00325399	55	0.058676	93	6.47927e-006	131	5.82587e-008
18	9.03421e-008	56	0.00912524	94	6.88612e-009	132	0.000267786
19	4.64258e-005	57	0.00979944	95	2.66498e-007	133	3.79111e-006
20	1.7759e-005	58	6.50723e-006	96	0.00018515	134	0.000186764
21	3.19185e-007	59	2.72368e-007	97	0.00131383	135	0.00126388
22	3.40523e-007	60	2.87616e-006	98	0.000941853	136	2.42698e-007
23	2.0202e-007	61	1.32635e-007	99	0.00255925	137	9.5766e-007
24	0.000228592	62	2.09192e-007	100	0.00778349	138	2.81062e-006
25	1.29468e-007	63	1.61541e-007	101	2.16464e-008	139	4.98905e-007
26	5.74663e-007	64	1.46775e-007	102	1.42101e-006	140	1.18904e-007
27	1.21284e-006	65	6.4128e-008	103	0.00218583	141	7.35656e-005
28	1.07054e-006	66	1.96935e-006	104	0.091904	142	0.000498747
29	1.7667e-006	67	0.00017577	105	0.073152	143	9.58059e-008
30	0.073152	68	6.33667e-008	106	8.79658e-005	144	2.65173e-006
31	0.0013283	69	4.07402e-005	107	6.94824e-005	145	6.14211e-008
32	0.0017886	70	3.00376e-005	108	1.03001e-006	146	3.73727e-008
33	0.000843417	71	4.0861e-005	109	0.000506209	147	6.6244e-006
34	7.17919e-008	72	2.50224e-007	110	4.38388e-006	148	0.00218583
35	2.76684e-009	73	0.00050105	111	4.94246e-007
36	2.50338e-007	74	6.97493e-005	112	4.48404e-007
37	8.73953e-009	75	0.000506731	113	3.65603e-008
Total log likelihood of joint reconstruction:							-1776.53

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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_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_a1b_d2 profile HMM generated consensus sequence
qvlfDSGTtfTyLlqpvYnAvrsaFtdqinakrtpvspplsaLdvCYklsvrltdgttv
rfPtvSlrFEGGaqmvseqppmLfIsrnegnvvCamGSsshmgmtanIIGniqQqnkrV
vYDlqRsrLGwaptqC

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

        Domain 1 of 1, from 4 to 122: score 31.4, E = 3.5e-10

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkk.a.fdp.SS.Y...v.C...
                    +D+G++ + ++ + + +a + ++t++++a+++p S++++  + C + 
AP_pepsins     4    FDSGTTFTYLLQPVY-NAVRSAFTDQInAkRTPvSPpLsalDvCykl 49   

                 ivtllsysqPssktsttaqdtirgagGqskiyvSklktsgqirknllslv
                 +v+l   +++++ +++t  +++r  gG  +++vS  + +++        +
AP_pepsins    50 SVRL---TDGTTVRFPT--VSLRFEGG--AQMVS--EQPPML-------F 83   

                 tikitkGnvTevenrslpsdgvflvvtdpedqksrydvILGrldfLrqln
                   +   Gnv    +++++s+   ++   +         I+G+  + +q +
AP_pepsins    84 ISRNE-GNV----VCAMGSS--SHMG--M------TANIIGN--IQQQNK 116  

                 svhidl<-*
                  v+ dl   
AP_pepsins   117 RVVYDL    122  

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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.