CAARD:NIX

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

(NIXMm:0.022522,NIXh3:0.056116,(NIXrn:0.019703,(NIXm:0.099440,NIXh:0.063818)N3:0.783648)N2:0.014616);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
NIXMm	N1	0.0225224	-
NIXh3	N1	0.0561161	-
NIXrn	N2	0.0197031	-
NIXm	N3	0.0994395	-
NIXh	N3	0.0638182	-
N1	root!	-	NIXMm NIXh3 N2
N2	N1	0.0146158	NIXrn N3
N3	N2	0.783648	NIXm NIXh

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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	0.0202733	27	0.000975997	54	0.000741882	81	0.0469483
1	0.0185284	28	7.95646e-006	55	0.000462605	82	0.0239413
2	0.0155666	29	2.47015e-005	56	0.00088901	83	0.0109203
3	0.0375775	30	0.0375775	57	0.00442	84	0.000163275
4	0.00030853	31	0.00704066	58	1.68968e-005	85	0.0195498
5	5.30978e-005	32	7.47067e-006	59	0.0109203	86	0.0144354
6	5.60797e-007	33	0.00144328	60	4.47274e-006	87	0.00428393
7	0.0117275	34	0.00309408	61	0.0224882	88	0.0185284
8	1.14307e-005	35	3.8607e-006	62	0.000824152	89	0.000625625
9	0.0159245	36	0.024009	63	0.0202733	90	0.00104718
10	0.0166649	37	0.0009179	64	0.0202733	91	0.000122076
11	1.60078e-005	38	0.000322545	65	0.0185284	92	0.00201443
12	0.00371798	39	0.052318	66	2.64657e-005	93	0.00442
13	0.0109203	40	0.0276989	67	9.04559e-005	94	1.08434e-005
14	0.00454267	41	0.000350537	68	0.000890541	95	1.86799e-006
15	6.36957e-006	42	0.0202733	69	0.000557693	96	0.000539514
16	0.018514	43	0.002392	70	1.10523e-005	97	0.0239413
17	0.0469483	44	0.0140227	71	0.0038335	98	0.00523597
18	0.0375775	45	0.00441014	72	0.000994813	99	0.000350906
19	0.0469483	46	0.0245096	73	0.0469483	100	0.000114797
20	1.41501e-007	47	0.000536866	74	0.0375775	101	0.000890541
21	2.28226e-005	48	2.18948e-005	75	0.0469483	102	0.0245096
22	0.00117634	49	7.38691e-007	76	0.0140227	103	0.00441014
23	0.0202733	50	0.0195498	77	0.0155666	104	0.024009
24	0.0276989	51	0.0193248	78	0.0469483	105	0.0208619
25	1.86201e-005	52	0.000238026	79	0.000906378	106	0.00454267
26	0.000543065	53	0.0375775	80	0.0166649	107	0.000484787
Total log likelihood of joint reconstruction:							-700.83

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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="nix" 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	0.0202962	27	0.000978563	54	0.000742743	81	0.0469547
1	0.0185373	28	1.50001e-005	55	0.000463535	82	0.023948
2	0.0155725	29	4.76717e-005	56	0.000890824	83	0.0109203
3	0.037579	30	0.037579	57	0.0044369	84	0.000163341
4	0.000309381	31	0.00706652	58	2.97644e-005	85	0.0466031
5	5.3114e-005	32	1.28732e-005	59	0.0109203	86	0.0369186
6	8.93113e-007	33	0.00144739	60	4.5053e-006	87	0.00429769
7	0.01173	34	0.00309743	61	0.0224983	88	0.0185373
8	2.33001e-005	35	6.82112e-006	62	0.000824988	89	0.000626462
9	0.0159398	36	0.0240098	63	0.0202962	90	0.00339208
10	0.0166744	37	0.000918566	64	0.0202962	91	0.00012801
11	1.60643e-005	38	0.000323241	65	0.0185373	92	0.00201622
12	0.00372211	39	0.0852464	66	3.49186e-005	93	0.0044369
13	0.0109203	40	0.053023	67	0.000137674	94	2.12701e-005
14	0.00455163	41	0.000350905	68	0.000893508	95	1.879e-006
15	8.97627e-006	42	0.0202962	69	0.000558238	96	0.000540384
16	0.0185191	43	0.00239681	70	1.1168e-005	97	0.023948
17	0.0469547	44	0.0140241	71	0.00383708	98	0.00525373
18	0.037579	45	0.0044191	72	0.000995167	99	0.000351299
19	0.0469547	46	0.0245212	73	0.0469547	100	0.000114917
20	2.80898e-007	47	0.000537363	74	0.037579	101	0.000893508
21	2.30876e-005	48	2.59912e-005	75	0.0469547	102	0.0245212
22	0.0011784	49	1.80935e-006	76	0.0140241	103	0.0044191
23	0.0202962	50	0.0466031	77	0.0155725	104	0.0240098
24	0.053023	51	0.0503953	78	0.0469547	105	0.0208631
25	2.80854e-005	52	0.000553225	79	0.000907227	106	0.00455163
26	0.000544716	53	0.037579	80	0.0166744	107	0.000485274
Total log likelihood of joint reconstruction:							-685.191

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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="nix" 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_nix profile HMM generated consensus sequence
VDTGtqyNlISaaCldRLGLkkrVKskkheGdklslPrtLKvVeQlElllITvGservd
CsAaVVDdnekelsLGLQTLlSLKCiINlDkehrvlrlKadkeElPFle

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

        Domain 1 of 1, from 1 to 88: score 28.2, E = 3.3e-09

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTG++  ++is+ c  +++lg                         
AP_nix         1    VDTGTQY-NLISAAC--LDRLG-----------------------L- 20   

                 sktsttaqdtirgagGqskiyvSklktsgqirkn..llslvtikitkGnv
                 +k+ +      + + G+ k       +++++ k+ ++l+l+ i +  G  
AP_nix        21 KKRVK-----SKKHEGD-KL------SLPRTLKVveQLELLLITV--G-- 54   

                 TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     +++  ++    vv+d e      ++ LG+ + L  l++  i l   
AP_nix        55 ----SERVDCS--AAVVDDNE-----KELSLGL-QTLLSLKCI-INL    88   

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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.