CAARD:Ty3

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

(Tse3:0.830919,Ty3-1:0.956100,Skipper:0.588788);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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<tbody> </tbody>

Name	Father	Distance to father	Sons
Tse1	N1	0.830919	-
Ty3-1	N1	0.9561	-
Skipper	N1	0.588788	-
N1	root!	-	Tse3 Ty3-1 Skipper

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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	7.71989e-005	25	0.000197835	50	0.000235168	75	0.00558699
1	0.00558699	26	0.035642	51	2.26278e-006	76	3.00531e-005
2	0.00116759	27	0.0387272	52	1.33903e-005	77	7.8373e-005
3	0.0167251	28	0.035642	53	0.00237575	78	1.56056e-005
4	0.000998097	29	0.0273101	54	0.0235569	79	0.0284149
5	9.53449e-005	30	0.0207853	55	1.40259e-005	80	2.10258e-006
6	5.76348e-006	31	3.72038e-005	56	4.43678e-005	81	1.1961e-005
7	0.00064337	32	0.00960596	57	0.000220013	82	2.32328e-005
8	0.00129452	33	0.000429207	58	0.000699845	83	0.000661695
9	0.00393664	34	0.0178833	59	0.0511587	84	0.000224075
10	2.32867e-005	35	0.000836329	60	0.0269838	85	0.000292944
11	0.000280749	36	6.22664e-006	61	5.07977e-005	86	1.8557e-005
12	0.000188518	37	0.000283318	62	0.00250357	87	0.000134017
13	0.000224075	38	0.0024893	63	0.000106614	88	0.000220013
14	0.00229075	39	0.000807913	64	1.83928e-005	89	7.06886e-005
15	0.0311865	40	0.0369598	65	0.0015744	90	0.000160821
16	0.000106397	41	0.000209914	66	2.40678e-006	91	0.00987787
17	1.6104e-005	42	0.00116132	67	0.000171445	92	8.71348e-005
18	0.000790744	43	4.49954e-005	68	0.000612459	93	0.000209213
19	0.000360959	44	7.46584e-005	69	0.00253491	94	0.000143405
20	7.02617e-006	45	0.0269838	70	0.026806	95	1.0105e-005
21	0.00031787	46	9.57991e-005	71	3.62511e-005	96	0.00980469
22	0.00240666	47	3.92123e-005	72	5.41616e-006	97	0.035642
23	3.22825e-005	48	0.0548966	73	0.00393664	98	0.00224607
24	0.000106397	49	0.00229075	74	0.00128771
Total log likelihood of joint reconstruction:							-765.621

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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="ty3" 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	0.000133337	25	0.000258713	50	0.000261812	75	0.00582981
1	0.00582981	26	0.058676	51	2.28664e-005	76	9.0268e-005
2	0.00143848	27	0.076748	52	3.01934e-005	77	0.000107424
3	0.0167867	28	0.058676	53	0.0060212	78	3.49869e-005
4	0.00141439	29	0.053761	54	0.051691	79	0.050901
5	0.000182798	30	0.042645	55	6.44088e-005	80	1.26421e-005
6	2.39601e-005	31	0.000122099	56	0.000116902	81	4.52553e-005
7	0.000892044	32	0.00963627	57	0.000292746	82	5.6791e-005
8	0.00148952	33	0.00118251	58	0.0024233	83	0.00130113
9	0.00428418	34	0.040752	59	0.091904	84	0.000362609
10	8.44392e-005	35	0.000931932	60	0.058676	85	0.000359292
11	0.000548246	36	2.51926e-005	61	5.55151e-005	86	4.81248e-005
12	0.00023138	37	0.000376669	62	0.00256728	87	0.000247219
13	0.000362609	38	0.0029416	63	0.000335607	88	0.000292746
14	0.00298341	39	0.000959675	64	2.57421e-005	89	0.000305842
15	0.068765	40	0.06183	65	0.00209525	90	0.000261778
16	0.000309543	41	0.000224952	66	8.7596e-006	91	0.0106581
17	5.01389e-005	42	0.00165049	67	0.000198519	92	0.000181839
18	0.000885199	43	0.000133314	68	0.0021354	93	0.000728355
19	0.000450825	44	0.000117706	69	0.0078053	94	0.000171039
20	2.39284e-005	45	0.058676	70	0.076748	95	3.40244e-005
21	0.000953115	46	0.000188206	71	0.000143974	96	0.0123828
22	0.00322298	47	0.000180976	72	1.57106e-005	97	0.058676
23	4.49889e-005	48	0.091904	73	0.00428418	98	0.00262784
24	0.000309543	49	0.00298341	74	0.00167473
Total log likelihood of joint reconstruction:							-700.61

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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="ty3" 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_Ty3 profile HMM generated consensus sequence
lDTGSstSFInkRlIqdmKyhVhqTfPlLdVKGFVeTkSnlIqhnvrvkIkhNfDLyee
ifyIIDslfqqvilGnsIfkqryPkiL

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

        Domain 1 of 1, from 1 to 85: score 42.2, E = 2e-13

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +DTG+s  s+i+k+  l+q +                      ++ +
AP_Ty3         1    LDTGSST-SFINKR--LIQDMK---------------------YHVH 23   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 + t++     +  ++G  ++      +s +i++n    v++ki+ +    
AP_Ty3        24 Q-TFP-----LLDVKGFVET------KSNLIQHN----VRVKIK-H---- 52   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                   n +l ++  +++++d  +     +vILG+  + +q +     +   
AP_Ty3        53 --NFDLYEE--IFYIIDSLF----QQVILGN-SIFKQRY---PKI    85   

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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.