CAARD:SASPase

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

(SASPase_Mo:0.162083,(SASPase_Ho:0.000000,SASPase_Pa:0.000000)N2:0.039731,(SASPase_Mu:0.049890,(SASPase_Bo:0.026389,SASPase_Ca:0.008329) N4:0.009664)N3:0.004968);

Top

Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide

Name	Father	Distance to father	Sons
SASPase_Monodelphis_domestica	N1	0.162083	-
SASPase_Homo_sapiens	N2	0	-
SASPase_Pan_troglodytes	N2	0	-
SASPase_Mus_musculus	N3	0.0498901	-
SASPase_Bos_taurus	N4	0.0263886	-
SASPase_Canis familiaris	N4	0.00832901	-
N1	root!	-	SASPase_Mo N2 N3
N2	N1	0.0397305	SASPase_Ho SASPase_Pa
N3	N1	0.00496793	SASPase_Mu N4
N4	N3	0.00966427	SASPase_Bo SASPase_Ca

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	0.0457152	22	0.00148054	44	0.0602493	66	0.0529372
1	0.0377861	23	0.0377861	45	1.63198e-005	67	0.044692
2	0.044692	24	0.0393332	46	0.01298	68	0.00242698
3	0.0602493	25	0.0752907	47	0.0377861	69	0.046703
4	0.0529372	26	0.000191977	48	0.0393332	70	0.046703
5	0.0298127	27	0.040926	49	1.39047e-009	71	0.0529372
6	0.0457152	28	0.0331559	50	0.00117269	72	0.0368726
7	0.044692	29	6.35817e-005	51	0.00210712	73	0.0368726
8	0.0457152	30	0.0290889	52	0.0752907	74	0.0602493
9	0.0457152	31	0.0457152	53	0.0602493	75	0.0393332
10	0.000155531	32	0.0457152	54	0.0448667	76	0.0377861
11	0.040926	33	0.0448667	55	9.66979e-007	77	0.0457152
12	3.24412e-008	34	0.0457152	56	0.000833189	78	0.0752907
13	0.0752907	35	0.0529372	57	0.00110034	79	0.0298127
14	0.01298	36	0.0290889	58	0.000833189	80	0.0377861
15	0.046703	37	0.0602493	59	0.0529372	81	0.0163232
16	0.000998968	38	0.0529372	60	5.17693e-007	82	0.000331506
17	0.00171922	39	0.046703	61	0.0331559	83	0.0529372
18	0.0393332	40	0.0167153	62	0.0752907	84	0.00011584
19	0.0377861	41	0.0448667	63	0.0457152	85	0.0752907
20	0.0602493	42	0.0368726	64	0.0529372	86	0.0377861
21	0.000470807	43	0.0752907	65	0.0290889	87	0.0331559
Total log likelihood of joint reconstruction:							-402.473

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="saspase" 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	0.0457156	22	0.00148087	44	0.0602493	66	0.0529374
1	0.0377862	23	0.0377862	45	1.71402e-005	67	0.0446921
2	0.0446921	24	0.0393333	46	0.01298	68	0.0024281
3	0.0602493	25	0.0752908	47	0.0377862	69	0.0467032
4	0.0529374	26	0.000192652	48	0.0393333	70	0.0467032
5	0.0298128	27	0.040926	49	3.60167e-009	71	0.0529374
6	0.0457156	28	0.0331559	50	0.00117401	72	0.0368728
7	0.0446921	29	6.35919e-005	51	0.00210802	73	0.0368728
8	0.0457156	30	0.029089	52	0.0752908	74	0.0602493
9	0.0457156	31	0.0457156	53	0.0602493	75	0.0393333
10	0.000155538	32	0.0457156	54	0.0448668	76	0.0377862
11	0.040926	33	0.0448668	55	9.6764e-007	77	0.0457156
12	8.18781e-008	34	0.0457156	56	0.000833307	78	0.0752908
13	0.0752908	35	0.0529374	57	0.00110081	79	0.0298128
14	0.01298	36	0.029089	58	0.000833307	80	0.0377862
15	0.0467032	37	0.0602493	59	0.0529374	81	0.0163232
16	0.000999219	38	0.0529374	60	5.19973e-007	82	0.000331538
17	0.00171966	39	0.0467032	61	0.0331559	83	0.0529374
18	0.0393333	40	0.0167153	62	0.0752908	84	0.000200982
19	0.0377862	41	0.0448668	63	0.0457156	85	0.0752908
20	0.0602493	42	0.0368728	64	0.0529374	86	0.0377862
21	0.000471383	43	0.0752908	65	0.029089	87	0.0331559
Total log likelihood of joint reconstruction:							-399.981

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="saspase" 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_saspase profile HMM generated consensus sequence
vDsGAqvsvvhPdLWEevtDGdlDtLrPFenvvKvAnGAEmKiLGvWDtkvsLGKlklk
AeFLvAnAsaEEAiiGtDvLqDHnAvLDF

Top

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

       Domain 1 of 1, from 1 to 88: score 55.6, E = 1.8e-17

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vD+GA+v sv+++++++  + g  ++                 ++P 
AP_saspase     1    VDSGAQV-SVVHPDLWEEVTDGDLDT-----------------LRPF 29   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    ++     +++a+G  ++     k++g +      ++++++  G    
AP_saspase    30 --ENV-----VKVANGA-EM-----KILGVW------DTKVSL--G---- 54   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                   + +l+ +  flv+ + ++     ++I+G  d+L+++n+v  d+   
AP_saspase    55 --KLKLKAE--FLVA-NASA----EEAIIGT-DVLQDHNAV-LDF    88   

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.