CAARD:COG5550

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

(RB280:0.746085,(SSO1395:0.457434,ST0709:0.380994)N2:0.217651,((all7265:0.579096, (PAE0993:0.413358,PAE0531:0.412493)N5:0.382074)N4:0.146186,(AF0612:0.797852, (SSO2164:0.412159,(SS01929:0.196241,SS01523:0.000589)N8:0.548989)N7:0.144960)N6:0.129051)N3:0.058060);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
RB280	N1	0.746085	-
SSO1395	N2	0.457434	-
ST0709	N2	0.380994	-
all7265	N4	0.579096	-
PAE0993	N5	0.413358	-
PAE0531	N5	0.412493	-
AF0612	N6	0.797852	-
SSO2164	N7	0.412159	-
SS01929	N8	0.196241	-
SS01523	N8	0.000589257	-
N1	root!	-	-
N2	N1	0.217651	-
N3	N1	0.0580597	-
N4	N3	0.146186	-
N5	N4	0.382074	-
N6	N3	0.129051	-
N7	N6	0.14496	-
N8	N7	0.548989	-

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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	2.07755e-007	32	0.0114254	64	1.12465e-010	96	3.41864e-011
1	6.16028e-006	33	0.00633147	65	4.6863e-007	97	0.000126396
2	2.84179e-005	34	5.99032e-005	66	6.26756e-014	98	0.00503064
3	0.00162644	35	5.73143e-013	67	4.16281e-010	99	1.16824e-012
4	5.7979e-007	36	4.87795e-010	68	8.52815e-014	100	0.00269989
5	1.17327e-010	37	0.000215497	69	9.18399e-011	101	1.05534e-009
6	0.00274713	38	1.10747e-009	70	1.77576e-012	102	1.14876e-008
7	1.63818e-011	39	3.22146e-013	71	8.2412e-010	103	3.33415e-006
8	0.0221475	40	2.29634e-013	72	0.00946478	104	6.58553e-012
9	1.16265e-009	41	1.16653e-014	73	0.00443233	105	3.18635e-011
10	4.36039e-010	42	3.00558e-014	74	0.00401331	106	1.1147e-009
11	7.79227e-010	43	8.0983e-013	75	1.46555e-011	107	5.35543e-007
12	3.48535e-009	44	4.56434e-011	76	8.94946e-015	108	4.38763e-010
13	5.96252e-016	45	3.7383e-010	77	3.18603e-006	109	5.35656e-012
14	2.81093e-011	46	5.02626e-014	78	3.37571e-010	110	9.44788e-013
15	0.00389872	47	2.66827e-007	79	1.11485e-009	111	4.54911e-010
16	2.83014e-009	48	1.74806e-006	80	8.27156e-014	112	0.00276597
17	7.85328e-010	49	6.62296e-015	81	0.00542996	113	5.74397e-011
18	7.93748e-013	50	2.06042e-008	82	0.00406087	114	3.69354e-011
19	1.07462e-007	51	2.1064e-009	83	1.66109e-007	115	1.38784e-005
20	0.000977573	52	3.14138e-010	84	2.00264e-010	116	4.35012e-007
21	5.70249e-005	53	5.08745e-012	85	2.39273e-012	117	6.2004e-009
22	4.65245e-010	54	8.00885e-012	86	1.85687e-015	118	8.63412e-011
23	9.09187e-005	55	3.866e-009	87	3.50557e-011	119	2.58201e-010
24	1.5792e-009	56	2.57977e-006	88	1.78112e-006	120	9.63224e-006
25	0.0114254	57	3.3233e-011	89	1.59469e-012	121	1.88822e-010
26	0.0120658	58	1.19256e-010	90	1.9257e-006	122	3.12042e-014
27	1.0173e-006	59	1.49794e-009	91	6.15001e-007	123	1.74136e-014
28	7.64498e-010	60	2.16886e-009	92	1.02648e-006	124	9.66364e-015
29	1.31444e-007	61	1.22629e-011	93	0.00162644	125	2.83992e-016
30	0.000187558	62	5.0934e-007	94	8.81775e-011
31	0.0203703	63	6.34388e-007	95	4.276e-010
Total log likelihood of joint reconstruction:							-2384.59

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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="cog5550" 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	3.26027e-007	32	0.040126	64	1.75613e-010	96	1.1148e-010
1	6.2885e-006	33	0.066005	65	3.39123e-006	97	0.000132659
2	2.88831e-005	34	0.00036467	66	3.87814e-013	98	0.051691
3	0.00162883	35	1.804e-012	67	7.52485e-010	99	5.88923e-012
4	6.68679e-007	36	9.85517e-010	68	1.1913e-012	100	0.068765
5	5.31867e-010	37	0.00180356	69	2.92944e-010	101	2.15313e-009
6	0.00352469	38	3.47166e-008	70	3.84059e-011	102	3.62088e-008
7	2.68261e-011	39	1.3709e-011	71	1.2703e-008	103	6.49747e-005
8	0.091904	40	6.25959e-012	72	0.06183	104	2.93241e-010
9	6.79276e-009	41	1.11971e-013	73	0.053761	105	9.21871e-011
10	3.09825e-009	42	3.45282e-013	74	0.058565	106	7.11178e-009
11	3.42832e-009	43	1.06651e-011	75	2.61063e-010	107	9.20531e-007
12	9.54289e-009	44	9.10074e-011	76	3.9142e-014	108	1.305e-009
13	5.53359e-015	45	2.36183e-009	77	8.57053e-005	109	1.90838e-011
14	3.88989e-011	46	1.25477e-013	78	8.71339e-010	110	7.8035e-012
15	0.053761	47	2.72383e-007	79	4.77677e-009	111	3.30683e-009
16	1.04919e-008	48	7.58499e-006	80	9.5676e-013	112	0.042645
17	1.6877e-009	49	4.73034e-014	81	0.0520384	113	1.5211e-010
18	3.55651e-012	50	9.93123e-008	82	0.068765	114	5.39737e-011
19	1.19602e-007	51	7.19671e-009	83	5.88856e-006	115	0.00034091
20	0.00584221	52	1.20571e-009	84	3.12541e-010	116	2.97634e-006
21	0.000555916	53	2.32515e-011	85	6.80113e-012	117	5.27331e-008
22	1.58166e-009	54	3.61172e-011	86	1.82965e-014	118	4.06358e-010
23	0.00219016	55	2.26234e-008	87	6.13497e-011	119	3.1414e-010
24	3.7401e-009	56	9.68935e-006	88	4.66399e-006	120	1.31871e-005
25	0.040126	57	6.03357e-010	89	1.12967e-011	121	8.67366e-010
26	0.050901	58	3.8868e-010	90	5.48459e-006	122	5.78527e-013
27	7.4096e-006	59	1.00293e-008	91	7.05281e-007	123	2.83184e-013
28	1.34019e-009	60	1.47587e-008	92	1.8015e-006	124	3.47157e-014
29	9.23977e-007	61	3.13167e-011	93	0.00162883	125	9.77076e-016
30	0.0026529	62	6.51112e-007	94	1.89476e-010
31	0.073152	63	1.54459e-005	95	9.02772e-010
Total log likelihood of joint reconstruction:							-2184.87

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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="cog5550" 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_cog5550 profile HMM generated consensus sequence
IDTGFnGylliPqeifdklpsleltdnreyttanGkikstvfatieIgnklnrdaarvl
afspviepnLLGtelLkklglridykdgklEKivldp

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

        Domain 1 of 1, from 1 to 84: score 42.9, E = 1.2e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTG + + +i++e  +++kl+                     ++ +
  AP_cog5550     1    IDTGFNGYLLIPQE--IFDKLPS--------------------LELT 25   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    ++        ++a+G  ki     k+++          ti+i  G    
  AP_cog5550    26 DNRE------YTTANG--KI-----KSTV-F-------ATIEI--G---- 48   

                   venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                       +l +d+  +v+  +p++     + +LG   +L++l+   id+   
  AP_cog5550    49 ---NKLNRDA-ARVLaFSPVI----EPNLLGT-ELLKKLGLR-IDY    84   

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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.