CAARD:Tat

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

(B1147A04:0.303325,(Cinful1:0.345617,Retrosor1:0.236405)N2:0.215906,((RIRE2:0.029132,Orizacinfu:0.075526)N4:0.230674,(Grande:0.522943, (Ogre:0.639515,(Tft1:0.337216,(Tat4-1:0.304526,Tft2:0.356348)N8:0.128821)N7:0.076434)N6:0.260180)N5:0.068321)N3:0.061040);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
B1147A04	N1	0.303325	-
Cinful1	N2	0.345617	-
Retrosor1	N2	0.236405	-
RIRE2	N4	0.0291318	-
Orizacinfu	N4	0.0755262	-
Grande	N5	0.522943	-
Ogre	N6	0.639515	-
Tft1	N7	0.337216	-
Tat4-1	N8	0.304526	-
Tft2	N8	0.356348	-
N1	root!	-	B1147A04 N2 N3
N2	N1	0.215906	Cinful1 Retrosor1
N3	N1	0.0610404	N4 N5
N4	N3	0.230674	RIRE2 Orizacinfu
N5	N3	0.0683211	Grande N6
N6	N5	0.26018	Ogre N7
N7	N6	0.0764342	Tft1 N8
N8	N7	0.128821	Tat4-1 Tft2

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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	1.41368e-006	29	4.86429e-018	58	4.66671e-013	87	9.63661e-005
1	0.000785818	30	3.01313e-008	59	1.6776e-011	88	1.38765e-012
2	2.27026e-008	31	0.000171151	60	5.89048e-010	89	1.73183e-006
3	0.00507483	32	1.04585e-008	61	4.28759e-015	90	2.15333e-007
4	2.01005e-005	33	6.2955e-015	62	4.566e-009	91	6.43821e-015
5	3.53726e-007	34	1.10903e-005	63	2.09022e-005	92	0.00050763
6	9.042e-009	35	0.000130426	64	1.2049e-005	93	1.44632e-008
7	1.6277e-007	36	3.19345e-009	65	1.34854e-012	94	2.46642e-009
8	1.53342e-006	37	1.6104e-011	66	7.30346e-006	95	3.91563e-006
9	1.88822e-008	38	1.03722e-006	67	4.68925e-011	96	9.83054e-015
10	5.7376e-007	39	3.00308e-015	68	0.00291627	97	7.05276e-012
11	1.97012e-013	40	1.34097e-010	69	9.43145e-011	98	5.91373e-006
12	6.42366e-014	41	7.82515e-017	70	8.80988e-005	99	3.06561e-008
13	1.80724e-009	42	0.00975184	71	1.03416e-009	100	8.17295e-011
14	1.29388e-006	43	5.14249e-013	72	8.9066e-005	101	1.48106e-009
15	4.09213e-012	44	3.81251e-009	73	1.00951e-011	102	1.89571e-005
16	2.37299e-012	45	2.91563e-009	74	1.23689e-015	103	2.97866e-011
17	6.63906e-010	46	0.00507483	75	2.92218e-014	104	6.42094e-007
18	6.28341e-012	47	2.81925e-011	76	5.31879e-012	105	4.41981e-015
19	0.0173312	48	2.13087e-005	77	0.000191414	106	5.95987e-013
20	7.19865e-011	49	5.66222e-013	78	1.15391e-006	107	4.05319e-014
21	9.95909e-015	50	8.3792e-006	79	2.58017e-008	108	8.94314e-005
22	1.59868e-014	51	1.15531e-006	80	1.30999e-005	109	8.15832e-011
23	7.32091e-016	52	2.38958e-006	81	4.15227e-007	110	1.57442e-012
24	8.13337e-016	53	0.00990247	82	0.00507483	111	6.29e-009
25	7.2796e-008	54	8.82727e-012	83	3.51539e-006	112	2.70596e-009
26	1.92834e-014	55	1.15501e-009	84	9.04621e-007	113	4.44276e-011
27	1.36162e-010	56	0.00507483	85	2.86482e-011	114	6.08058e-006
28	3.05747e-008	57	1.87889e-011	86	6.31577e-006
Total log likelihood of joint reconstruction:							-2231.98

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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="mag" 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	3.6725e-006	29	2.25569e-016	58	6.98006e-012	87	0.000462618
1	0.000790939	30	1.6841e-007	59	4.21865e-011	88	3.63272e-012
2	3.64004e-008	31	0.000171607	60	2.02251e-009	89	8.21749e-006
3	0.00507721	32	4.94875e-008	61	1.81827e-014	90	2.90049e-007
4	2.06099e-005	33	3.11238e-014	62	1.87911e-008	91	2.24241e-014
5	9.00976e-007	34	1.1297e-005	63	3.45323e-005	92	0.000510622
6	2.59392e-008	35	0.000379112	64	1.60915e-005	93	2.8276e-008
7	2.47309e-007	36	6.71391e-009	65	1.66128e-011	94	7.03625e-009
8	3.59597e-006	37	4.60679e-011	66	3.48913e-005	95	5.55346e-006
9	3.01302e-008	38	1.0604e-006	67	3.63827e-010	96	1.47975e-013
10	5.76851e-007	39	8.01785e-014	68	0.00291829	97	4.07826e-011
11	7.22958e-013	40	4.95242e-010	69	4.52588e-010	98	8.20857e-006
12	3.57058e-013	41	8.2508e-016	70	9.82203e-005	99	4.69936e-008
13	3.0699e-009	42	0.051691	71	1.65234e-009	100	8.52691e-011
14	1.6756e-006	43	8.07757e-012	72	9.04857e-005	101	4.28075e-009
15	1.89075e-011	44	7.3326e-009	73	7.70404e-011	102	1.9261e-005
16	3.32507e-011	45	3.78818e-009	74	3.89697e-015	103	4.03253e-011
17	7.06141e-010	46	0.00507721	75	5.55726e-013	104	6.47817e-007
18	2.30741e-011	47	1.15373e-010	76	9.9636e-012	105	4.67254e-014
19	0.06183	48	2.59197e-005	77	0.000193033	106	2.33224e-012
20	1.74411e-010	49	1.5318e-012	78	1.17323e-006	107	7.7275e-013
21	4.65163e-014	50	8.94634e-006	79	4.13205e-008	108	8.99998e-005
22	4.80621e-014	51	1.18273e-006	80	1.39044e-005	109	1.8569e-010
23	1.42906e-015	52	3.27771e-006	81	6.86813e-007	110	7.55878e-012
24	8.35835e-015	53	0.053761	82	0.00507721	111	2.13339e-008
25	1.84309e-007	54	4.56922e-011	83	3.9448e-006	112	6.78394e-009
26	6.90828e-014	55	2.21269e-009	84	9.55472e-007	113	6.82608e-011
27	1.63109e-010	56	0.00507721	85	1.11599e-010	114	6.16635e-006
28	3.50803e-008	57	1.01897e-010	86	1.37113e-005
Total log likelihood of joint reconstruction:							-2121.62

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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="mag" 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_tat profile HMM generated consensus sequence
vDtGSslnvlfaktLqqmgverselqpsqsPliGvfpgetlmplGtItLPVtfGttenf
rTehvsFeVvDleaaYnaILGRPwLhakfkAvpstlhlcmKmpsprGvitvrG

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

       Domain 1 of 1, from 1 to 93: score 65.0, E = 2.8e-20

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTG+s+ +v+ +    +q++g +r++                +qPs
AP_tat         1    VDTGSSL-NVLFAK--TLQQMGVERSE----------------LQPS 28   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +s++    i ++ G++ +      ++g+        +t+ +t+G+ Te
AP_tat        29 --QSPL----IGVFPGETLM------PLGT--------ITLPVTFGT-TE 57   

                 venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                 +++++++s   f vv d+e+   +y++ILGr ++L +++++++     
AP_tat        58 NFRTEHVS---FEVV-DLEA---AYNAILGR-PWL-HAKFKAVPS    93   

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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.