CAARD:412 mdg1

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

(N1:0.0,412:0.300000);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
412	N1	0.3	-
Mdg1	N1	0.3	-
N1	root!	-	412 Mdg1

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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	0.00197082	22	0.000673976	44	0.0358474	66	0.0330756
1	0.028196	23	0.0201276	45	0.000992501	67	0.000204135
2	0.0269084	24	0.000673976	46	2.74472e-005	68	0.028196
3	0.0498761	25	0.0011932	47	0.0011932	69	0.0498761
4	0.0372241	26	0.0201276	48	0.00202552	70	0.0259827
5	0.00405512	27	0.0259827	49	0.00102642	71	0.0259827
6	0.0259827	28	0.000314974	50	8.54331e-005	72	0.0498761
7	0.0297219	29	0.0498761	51	0.00230045	73	0.00197082
8	0.00197082	30	0.0259827	52	0.0259827	74	0.028196
9	0.0621819	31	0.0498761	53	0.0330756	75	0.0275402
10	0.0347441	32	0.0220105	54	0.000702156	76	0.0259827
11	2.38116e-005	33	0.000196896	55	0.00405512	77	0.0347441
12	0.000248302	34	0.000673976	56	0.0275402	78	0.0347441
13	0.00210886	35	0.0259827	57	0.0117064	79	0.0224481
14	0.00173055	36	0.0220105	58	0.00197082	80	0.0201276
15	0.00102642	37	0.0297219	59	0.032548	81	0.0141207
16	0.00189948	38	0.000364737	60	0.000113966	82	6.52615e-005
17	0.00210886	39	0.0498761	61	0.00102642	83	0.00197082
18	0.00173055	40	0.000253439	62	0.0201276	84	0.00405512
19	0.00197082	41	0.000342861	63	0.0275402	85	0.00189948
20	0.00030487	42	8.97346e-005	64	0.0330756
21	0.000108934	43	0.00197082	65	0.0259827
Total log likelihood of joint reconstruction:							-465.369

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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="412_mdg1" 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	0.00479559	22	0.00148284	44	0.0366289	66	0.0332631
1	0.028886	23	0.0205182	45	0.00219789	67	0.000453979
2	0.0276271	24	0.00148284	46	8.03607e-005	68	0.028886
3	0.050169	25	0.00263986	47	0.00263986	69	0.050169
4	0.0382672	26	0.0205182	48	0.00406281	70	0.0269992
5	0.0083426	27	0.0269992	49	0.00232551	71	0.0269992
6	0.0269992	28	0.000818564	50	0.00023484	72	0.050169
7	0.0307625	29	0.050169	51	0.0049056	73	0.00479559
8	0.00479559	30	0.0269992	52	0.0269992	74	0.028886
9	0.0628339	31	0.050169	53	0.0332631	75	0.0277081
10	0.0353273	32	0.0222665	54	0.00154784	76	0.0269992
11	7.35313e-005	33	0.00057839	55	0.0083426	77	0.0353273
12	0.000767354	34	0.00148284	56	0.0277081	78	0.0353273
13	0.00437808	35	0.0269992	57	0.0118167	79	0.0225776
14	0.00373254	36	0.0222665	58	0.00479559	80	0.0205182
15	0.00232551	37	0.0307625	59	0.0338425	81	0.0141382
16	0.0038781	38	0.000908252	60	0.000321467	82	0.000217822
17	0.00437808	39	0.050169	61	0.00232551	83	0.00479559
18	0.00373254	40	0.000652718	62	0.0205182	84	0.0083426
19	0.00479559	41	0.00111944	63	0.0277081	85	0.0038781
20	0.000765612	42	0.000265058	64	0.0332631
21	0.000346017	43	0.00479559	65	0.0269992
Total log likelihood of joint reconstruction:							-426.644

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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="412_mdg1" 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_412_mdg1 profile HMM generated consensus sequence
iDtGAdisiLKcnnnnlnniqpknkiniqGiGqqkiqsrGqthiEmcignyviPhdFHi
vpnnFPiPcDGiiGiDFiKKYnCqidf

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

         domain 1 of 1, from 1 to 86: score 73.1, E = 9.6e-23

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA++ s+++++  + + l                       qP+
  AP_412_mdg     1    IDTGADI-SILKCN--NNN-LNN--------------------IQPK 23   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +k++      i+g+ Gq+ki     ++ gq++      ++ +i  G    
  AP_412_mdg    24 NKIN------IQGI-GQQKI-----QSRGQTH------IEMCI--G---- 49   

                   venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                     n+ +p+d  f++v+ +  +   ++d+I+G+ df +++n+  id+   
  AP_412_mdg    50 --NYVIPHD--FHIVpNNFPI---PCDGIIGI-DFIKKYNCQ-IDF    86   

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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.