CAARD:Galadriel

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

(Monkey:0.345284,Tntom1:0.656479,Galadriel:0.416213);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Monkey	N1	0.345284	-
Tntom1	N1	0.656479	-
Galadriel	N1	0.416213	-
N1	root!	-	Monkey Tntom1 Galadriel

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Jpf output: Joint probability per amino acid position and total Log Likelihood

<tbody>

Position	Joint probability	Position	Joint probability	Position	Joint probability	Position	Joint probability
0	0.00435265	22	4.39034e-005	44	8.86582e-005	66	0.0128943
1	0.0128943	23	0.017482	45	0.0132419	67	0.0166531
2	0.00973624	24	0.00142395	46	0.00142169	68	0.000811327
3	0.0298774	25	0.000587456	47	0.000229269	69	0.00045092
4	0.0145309	26	0.00142395	48	0.000360186	70	0.0102745
5	0.00973624	27	2.59725e-005	49	0.000133929	71	0.0031658
6	0.00475066	28	0.000414224	50	0.0116207	72	0.00076531
7	0.000505551	29	0.017482	51	0.0298774	73	0.000168744
8	0.00190066	30	0.000210086	52	1.78049e-005	74	0.00283365
9	0.000542969	31	0.00435265	53	0.000138536	75	0.0166531
10	0.000347887	32	0.00746587	54	2.43072e-005	76	0.0011319
11	1.66899e-005	33	0.00139974	55	0.0298774	77	0.000348528
12	8.23347e-005	34	1.20178e-005	56	0.000550171	78	1.53855e-005
13	1.03668e-006	35	0.00131341	57	1.68356e-006	79	9.15489e-006
14	0.00205483	36	0.000590409	58	0.00746587	80	6.70009e-005
15	2.48664e-005	37	1.75236e-005	59	0.0011319	81	1.58093e-005
16	3.97823e-005	38	0.00424187	60	0.000121839	82	0.00088152
17	0.037141	39	3.19577e-005	61	0.00108207	83	0.0185498
18	0.0298774	40	0.0298774	62	0.000514005	84	1.28354e-005
19	0.037141	41	0.000133148	63	0.000226639
20	2.98646e-005	42	0.0145309	64	0.00311011
21	0.0031658	43	6.14778e-006	65	0.000633224
Total log likelihood of joint reconstruction:							-616.675

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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="galadriel" 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	0.00497409	22	9.57164e-005	44	0.000135022	66	0.0130085
1	0.0130085	23	0.0175711	45	0.0135196	67	0.01667
2	0.00981198	24	0.00154107	46	0.00151179	68	0.000951385
3	0.0298983	25	0.000598378	47	0.000413108	69	0.00100821
4	0.0146619	26	0.00154107	48	0.000397726	70	0.0104607
5	0.00981198	27	3.56048e-005	49	0.000201102	71	0.00332276
6	0.00475666	28	0.000565964	50	0.014261	72	0.000782294
7	0.000561782	29	0.0175711	51	0.0298983	73	0.000333559
8	0.00199282	30	0.000323998	52	5.37441e-005	74	0.0035152
9	0.0010246	31	0.00497409	53	0.000138849	75	0.01667
10	0.000393308	32	0.00749741	54	4.74739e-005	76	0.00139377
11	2.77674e-005	33	0.0017325	55	0.0298983	77	0.000405723
12	0.000185435	34	3.21234e-005	56	0.000606874	78	5.15036e-005
13	3.20461e-006	35	0.00141648	57	4.6506e-006	79	2.14636e-005
14	0.00219873	36	0.000680143	58	0.00749741	80	0.000108802
15	4.43253e-005	37	5.73834e-005	59	0.00139377	81	5.46793e-005
16	4.94017e-005	38	0.00476255	60	0.000123973	82	0.000986007
17	0.0372331	39	8.07984e-005	61	0.00129798	83	0.0185611
18	0.0298983	40	0.0298983	62	0.000647968	84	3.18518e-005
19	0.0372331	41	0.000309339	63	0.000233134
20	4.74741e-005	42	0.0146619	64	0.00327119
21	0.00332276	43	1.18557e-005	65	0.000702216
Total log likelihood of joint reconstruction:							-591.802

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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="galadriel" 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_galadriel profile HMM generated consensus sequence
vDTGATHnFiavreaqrLGLtlgKspshvKavNskaqpisGlAngVpikiWGnwgGnhN
LmvvpldDFeiIlgleFLrqakfvPm

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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 68.4, E = 2.5e-21

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGA++ ++i  +  +aq+lgl                    ++++
AP_galadri     1    VDTGATH-NFIAVR--EAQRLGL--------------------TLGK 24   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 s +s+     +++++ ++++     ++sg+ +      v iki+ G    
AP_galadri    25 S-PSH-----VKAVN-SKAQ-----PISGLANG-----VPIKIW-G---- 52   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                   n+   ++   +vv +++d    +++ILG+  fLrq+++  + +   
AP_galadri    53 --NWGGNHN--LMVV-PLDD----FEIILGL-EFLRQAKF--VPM    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.