CAARD:Chrofung

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

(AfRTL-1:0.451026,((Sushi-ichi:0.424181,FLJ38865:0.498614)N3:0.104446,(((Real:0.097092,Pyggy:0.157758)N6:0.599071, (MGLR3:0.677039,Grasshoppe:0.705748)N7:0.121776)N5:0.228167,(marY1:0.445998,(Dane-1:0.299148,Maggy:0.372394)N9:0.219832) N8:0.120816)N4:0.062005)N2:0.052318,(Cft-1:0.438641,(Skippy:0.481008,(Cgret:0.271134,Pyret:0.415548)N12:0.159519) N11:0.120020)N10:0.022517);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
AfRTL-1	N1	0.451026	-
Sushi-ichi	N3	0.424181	-
FLJ38865	N3	0.498614	-
Real	N6	0.0970923	-
Pyggy	N6	0.157758	-
MGLR3	N7	0.677039	-
Grasshopper	N7	0.705748	-
marY1	N8	0.445998	-
Dane-1	N9	0.299148	-
Maggy	N9	0.372394	-
Cft-1	N10	0.438641	-
Skippy	N11	0.481008	-
Cgret	N12	0.271134	-
Pyret	N12	0.415548	-
N1	root!	-	AfRTL-1 N2 N10
N2	N1	0.0523177	N3 N4
N3	N2	0.104446	Sushi-ichi FLJ38865
N4	N2	0.0620054	N5 N8
N5	N4	0.228167	N6 N7
N6	N5	0.599071	Real Pyggy
N7	N5	0.121776	MGLR3 Grasshopper
N8	N4	0.120816	marY1 N9
N9	N8	0.219832	Dane-1 Maggy
N10	N1	0.0225166	Cft-1 N11
N11	N10	0.12002	Skippy N12
N12	N11	0.159519	Cgret Pyret

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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	6.96521e-012	29	5.63431e-006	58	1.11242e-014	87	8.48126e-013
1	2.99163e-005	30	5.8997e-020	59	7.91262e-011	88	9.00218e-016
2	6.4363e-013	31	6.86135e-017	60	6.50687e-016	89	3.88161e-006
3	0.000611746	32	8.2396e-017	61	6.03764e-013	90	2.69027e-011
4	5.37956e-011	33	1.47077e-017	62	2.40961e-005	91	2.57814e-014
5	1.10803e-018	34	6.0759e-016	63	3.27651e-011	92	3.03955e-018
6	4.54225e-015	35	1.7766e-015	64	6.45036e-020	93	2.22102e-013
7	0.00673448	36	1.48712e-005	65	1.04379e-012	94	0.000597088
8	3.37886e-013	37	0.00142982	66	2.44491e-009	95	1.19173e-019
9	3.25244e-009	38	3.47026e-007	67	0.00435159	96	7.43072e-019
10	1.32022e-015	39	0.021522	68	2.91675e-013	97	6.81437e-017
11	2.62427e-013	40	0.00549305	69	2.00401e-016	98	5.41389e-014
12	0.000125576	41	0.00558476	70	3.16546e-005	99	3.29835e-013
13	2.44626e-015	42	0.00306596	71	9.93053e-015	100	5.20568e-011
14	4.21066e-018	43	1.67069e-017	72	2.56874e-019	101	3.97884e-006
15	4.91987e-019	44	5.36748e-019	73	0.000123741	102	0.000611746
16	0.00480454	45	2.61699e-013	74	1.21277e-018	103	1.22286e-018
17	2.09723e-011	46	0.00436893	75	2.43079e-021	104	4.40025e-010
18	4.57539e-017	47	1.10687e-017	76	1.20693e-018	105	2.09631e-005
19	7.17581e-013	48	2.39271e-018	77	1.57929e-011	106	1.92092e-006
20	1.46761e-021	49	9.40023e-014	78	7.66126e-010	107	1.95152e-018
21	3.82028e-010	50	3.83206e-010	79	7.743e-011	108	1.17129e-018
22	0.00412729	51	6.50424e-006	80	1.60286e-009	109	1.75118e-013
23	1.36299e-011	52	7.43899e-014	81	2.49756e-009	110	3.68142e-012
24	1.55643e-007	53	7.00419e-019	82	1.31633e-014	111	3.07423e-009
25	2.81773e-019	54	2.32332e-015	83	8.6209e-013	112	4.51984e-019
26	9.04411e-005	55	0.000107921	84	3.37746e-018	113	6.92431e-010
27	0.000139721	56	0.0054601	85	7.05266e-015	114	7.1995e-013
28	1.14347e-006	57	9.32844e-009	86	2.84114e-010	115	7.73632e-01
Total log likelihood of joint reconstruction:							-2984.13

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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="chrofung" 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	3.21334e-011	29	2.50382e-005	58	5.99881e-014	87	2.43806e-012
1	3.04932e-005	30	2.70898e-018	59	4.05537e-010	88	4.56042e-015
2	1.11564e-012	31	1.40119e-016	60	2.80234e-014	89	7.17312e-006
3	0.000612571	32	4.42008e-016	61	4.22258e-012	90	1.1543e-010
4	9.35929e-011	33	4.43102e-016	62	0.000875037	91	2.39245e-013
5	3.59806e-018	34	1.5729e-015	63	9.05764e-011	92	5.19499e-017
6	1.00491e-014	35	6.53542e-014	64	5.51501e-019	93	1.02354e-012
7	0.0334023	36	0.000379783	65	1.26682e-012	94	0.00112001
8	1.1717e-011	37	0.022944	66	7.41494e-009	95	2.24702e-018
9	4.50297e-009	38	3.52636e-007	67	0.0270901	96	1.20699e-017
10	8.89342e-015	39	0.091904	68	2.28252e-012	97	1.7334e-016
11	1.3543e-012	40	0.051544	69	3.79163e-015	98	2.05481e-013
12	0.00280765	41	0.051691	70	0.000839536	99	2.70759e-012
13	4.30616e-014	42	0.068765	71	1.19545e-014	100	3.01772e-010
14	2.57082e-016	43	2.76551e-016	72	1.59289e-018	101	4.21757e-006
15	6.52936e-017	44	7.44151e-018	73	0.00280235	102	0.000612571
16	0.019803	45	2.29027e-012	74	1.0414e-017	103	3.24146e-018
17	2.76313e-011	46	0.0393812	75	1.26663e-019	104	4.62672e-010
18	7.1694e-016	47	1.59461e-016	76	1.85088e-017	105	2.09876e-005
19	1.35016e-011	48	9.36587e-017	77	1.58403e-010	106	3.42887e-006
20	2.00756e-020	49	1.51029e-013	78	1.04432e-009	107	1.65337e-017
21	1.15196e-009	50	6.86563e-010	79	4.52779e-009	108	1.98214e-017
22	0.040752	51	6.5828e-006	80	4.39152e-009	109	9.71044e-013
23	2.90444e-011	52	1.16809e-012	81	3.70147e-008	110	2.16171e-011
24	6.54566e-007	53	1.09488e-017	82	5.28768e-014	111	7.76067e-009
25	3.16029e-018	54	2.16029e-014	83	1.02232e-012	112	7.51187e-018
26	0.000668521	55	0.000344082	84	2.93773e-017	113	1.30337e-009
27	0.00144386	56	0.0146818	85	5.47914e-014	114	2.16043e-012
28	1.38961e-005	57	3.20944e-008	86	8.22979e-009	115	3.01082e-012
Total log likelihood of joint reconstruction:							-2770.17

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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="chrofung" 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_chrofung profile HMM generated consensus sequence
iDSGAdgnfidprvVnkrRlplplkkePlqlegvDGrklEsGkItretapltlrihGnH
ieetafdFvidlarydiiLGmPWLekhnPtidw

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

       Domain 1 of 1, from 1 to 92: score 60.0, E = 8.9e-19

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+GA+  ++i +++++  +l+l                      P+
AP_chrofun     1    IDSGADG-NFIDPRVVNKRRLPL----------------------PL 24   

                 sktsttaqdtirgagGqskiyvSklktsgqirkn..llslvtikitkGnv
                 +k   +    + g++G+ k        sg+i +++ +   +t++i+ G  
AP_chrofun    25 KKEPLQ----LEGVDGR-KL------ESGKITREtaP---LTLRIH-G-- 57   

                 TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                     n+ + +   f  v+d+ +    yd+ILG+ ++L+++n+  id+   
AP_chrofun    58 ----NHIEETA--FDFVIDLAR----YDIILGM-PWLEKHNPT-IDW    92

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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.