CAARD:CRM

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

(Cereba:0.256601,CRM:0.108854,Beetle1:0.406445);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Cereba	N1	0.256601	-
CRM	N1	0.108854	-
Beetle1	N1	0.406445	-
N1	root!	-	Cereba CRM Beetle1

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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	0.0211493	23	0.00219101	46	0.000448108	69	0.0128177
1	0.0237575	24	0.00965986	47	0.00345732	70	5.74948e-005
2	0.0447096	25	0.0292434	48	5.61624e-005	71	0.00345732
3	0.0447096	26	0.000229695	49	0.0247346	72	0.0556344
4	0.0234289	27	0.0292434	50	0.000766687	73	0.0556344
5	0.0128177	28	0.0202687	51	0.000430744	74	0.0447096
6	0.00107028	29	1.16331e-005	52	0.00155438	75	0.0239428
7	0.016253	30	0.00230716	53	0.0344521	76	0.0292434
8	0.00284504	31	0.00103811	54	0.00179417	77	6.47616e-005
9	0.0303115	32	0.0112058	55	0.0202687	78	0.0184639
10	0.0234289	33	0.00143906	56	1.34949e-005	79	0.000605286
11	7.12784e-005	34	0.016253	57	0.00134632	80	0.0237575
12	7.50523e-005	35	0.00193199	58	1.45485e-006	81	0.000119544
13	0.00967887	36	0.0410283	59	0.0266469	82	0.000263106
14	0.0266469	37	0.0447096	60	0.000121758	83	3.04263e-006
15	0.030706	38	0.000808785	61	0.0128177	84	1.1687e-005
16	0.0299323	39	0.0266469	62	0.0237575	85	0.00965986
17	0.0556344	40	3.92484e-005	63	0.000229571	86	1.16958e-005
18	7.18365e-005	41	0.000178452	64	0.0266469	87	0.0447096
19	0.000287918	42	0.000106535	65	0.0292434	88	0.0239428
20	0.000774508	43	0.00253197	66	0.00967887	89	0.000780781
21	0.0215728	44	3.72616e-006	67	1.67007e-005
22	3.47091e-006	45	0.00257779	68	0.0303115
Total log likelihood of joint reconstruction:							-550.235

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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="crm" 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	0.0211946	23	0.00220946	46	0.000450598	69	0.0128178
1	0.0237825	24	0.00966114	47	0.00377161	70	6.70508e-005
2	0.0447133	25	0.0292455	48	6.51791e-005	71	0.00377161
3	0.0447133	26	0.000231616	49	0.0247376	72	0.0556509
4	0.0234574	27	0.0292455	50	0.00101961	73	0.0556509
5	0.0128178	28	0.020271	51	0.000436796	74	0.0447133
6	0.00108243	29	1.29072e-005	52	0.00158791	75	0.023957
7	0.0162604	30	0.00235212	53	0.051544	76	0.0292455
8	0.00288471	31	0.00105534	54	0.00191734	77	6.4937e-005
9	0.0303406	32	0.0112058	55	0.020271	78	0.0184679
10	0.0234574	33	0.00149828	56	2.66028e-005	79	0.000607247
11	7.44576e-005	34	0.0162604	57	0.00140683	80	0.0237825
12	9.64097e-005	35	0.00196607	58	2.04142e-006	81	0.000130744
13	0.00968003	36	0.0414349	59	0.0267146	82	0.0002917
14	0.0267146	37	0.0447133	60	0.00012316	83	3.87822e-006
15	0.0307384	38	0.000815057	61	0.0128178	84	1.40677e-005
16	0.0299508	39	0.0267146	62	0.0237825	85	0.00966114
17	0.0556509	40	4.01818e-005	63	0.000233756	86	1.35497e-005
18	0.000123627	41	0.00018162	64	0.0267146	87	0.0447133
19	0.000291539	42	0.000107861	65	0.0292455	88	0.023957
20	0.000786843	43	0.00269158	66	0.00968003	89	0.00101685
21	0.0215902	44	6.88599e-006	67	2.49929e-005
22	5.75137e-006	45	0.00262083	68	0.0303406
Total log likelihood of joint reconstruction:							-544.031

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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="crm" folder="mrof"></align>

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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.

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HMMs

>AP_crm profile HMM generated consensus sequence
iDGGsCnnlAssdmvEKLslttkpHPkPYkiqWlnnsGkvkvtklvrisFsigdsYsdv
vdCDvvPmdACniLLGRPwqfDketvHnGRt

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

        Domain 1 of 1, from 1 to 90: score 53.1, E = 1e-16

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D G++  +++s +  +++kl lt                   ++P+
AP_crm         1    IDGGSCN-NLASSD--MVEKLSLT-------------------TKPH 25   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                  k+ +     i+  +++ k+     k++ ++r      ++++i  G    
AP_crm        26 PKPYK-----IQWLNNSGKV-----KVTKLVR------ISFSI--G---- 53   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvh.idl<-*
                  +++s + d  + vv ++++    ++++LGr ++  ++++vh+++    
AP_crm        54 -DSYSDVVD--CDVV-PMDA----CNILLGR-PWQFDKETVHnGRT    90   

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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.