CAARD:COG3577

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

(Cc1307:0.377680,((Rc1339:0.011470,Rp867:0.022462)N3:0.419820,(Mmc12119:0.415269,rsph03003184:0.527451)N4:0.097539)N2:0.047189, (Atu1893:0.359069,((BR0864:0.251268,Mlr0565:0.350268)N7:0.092589,(((Atu0134:0.383832,(mll3161:0.414329, (bll8127:0.075244,Rpal1816:0.114557)N12:0.283918)N11:0.018694)N10:0.070693,(((PSPTO4961:0.141716,Pflu0200192:0.175463)N15:0.067453, (PA4965:0.228253,Mdeg02000624:0.279390)N16:0.041548)N14:0.278354,(PA4048:0.371880,Mdeg2586:0.361203)N17:0.132412)N13:0.058496) N9:0.062732,(Magn03006869:0.357174,bll3736:0.460751)N18:0.039089)N8:0.037214)N6:0.023450)N5:0.017432);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
Cc1307	N1	0.37768	-
Rc1339	N3	0.0114698	-
Rp867	N3	0.0224624	-
Mmc12119	N4	0.415269	-
rsph03003184	N4	0.527451	-
Atu1893	N5	0.359069	-
BR0864	N7	0.251268	-
Mlr0565	N7	0.350268	-
Atu0134	N10	0.383832	-
mll3161	N11	0.414329	-
bll8127	N12	0.0752442	-
Rpal1816	N12	0.114557	-
PSPTO4961	N15	0.141716	-
Pflu0200192	N15	0.175463	-
PA4965	N16	0.228253	-
Mdeg02000624	N16	0.27939	-
PA4048	N17	0.37188	-
Mdeg2586	N17	0.361203	-
Magn03006869	N18	0.357174	-
bll3736	N18	0.460751	-
N1	root!	-	Cc1307 N2 N5
N2	N1	0.0471895	N3 N4
N3	N2	0.41982	Rc1339 Rp867
N4	N2	0.097539	Mmc12119 rsph03003184
N5	N1	0.0174322	Atu1893 N6
N6	N5	0.0234503	N7 N8
N7	N6	0.0925895	BR0864 Mlr0565
N8	N6	0.0372135	N9 N18
N9	N8	0.0627316	N10 N13
N10	N9	0.0706931	Atu0134 N11
N11	N10	0.0186936	mll3161 N12
N12	N11	0.283918	bll8127 Rpal1816
N13	N9	0.0584961	N14 N17
N14	N13	0.278354	N15 N16
N15	N14	0.0674532	PSPTO4961 Pflu0200192
N16	N14	0.0415478	PA4965 Mdeg02000624
N17	N13	0.132412	PA4048 Mdeg2586
N18	N8	0.0390885	Magn03006869 bll3736

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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	1.34364e-012	24	4.2925e-014	48	2.07769e-025	72	1.0147e-025
1	2.90306e-005	25	1.83544e-020	49	7.87371e-011	73	2.81024e-016
2	3.77638e-006	26	2.27405e-018	50	0.00554436	74	0.000718715
3	0.000626383	27	3.66563e-027	51	0.000626383	75	1.80493e-006
4	9.71817e-006	28	5.75185e-029	52	1.11159e-024	76	0.000626383
5	5.10395e-012	29	1.04937e-025	53	9.67224e-013	77	3.02248e-011
6	1.26217e-018	30	1.8705e-018	54	1.9165e-030	78	1.72286e-010
7	5.141e-010	31	6.91318e-022	55	7.91261e-020	79	1.11666e-011
8	2.50935e-010	32	3.77638e-006	56	1.48236e-024	80	1.33506e-006
9	1.7462e-010	33	9.71817e-006	57	1.82131e-019	81	1.733e-024
10	1.28074e-014	34	7.55174e-010	58	6.38476e-010	82	9.35557e-020
11	1.09013e-028	35	0.000626383	59	1.36148e-026	83	2.67312e-009
12	2.77921e-023	36	4.65715e-030	60	3.14522e-009	84	1.19468e-022
13	6.82716e-023	37	4.14636e-019	61	3.50348e-006	85	9.67403e-015
14	2.03269e-007	38	8.67155e-021	62	4.95522e-020	86	2.13655e-018
15	5.99471e-024	39	6.12418e-012	63	7.59926e-011	87	2.32462e-025
16	1.66507e-018	40	2.53558e-015	64	2.7215e-022	88	4.30445e-019
17	4.74294e-012	41	3.92302e-018	65	8.76625e-012	89	3.68866e-019
18	2.38933e-007	42	1.64685e-013	66	8.94932e-020	90	3.60279e-026
19	6.18681e-016	43	2.32981e-025	67	6.81069e-013	91	4.8159e-012
20	1.87162e-020	44	2.66095e-014	68	2.80309e-014	92	7.89454e-029
21	1.41325e-024	45	1.00654e-019	69	1.19102e-028	93	6.57926e-013
22	5.33077e-023	46	1.60287e-024	70	3.23107e-012	94	8.52671e-019
23	1.19371e-020	47	9.22306e-013	71	1.96607e-019	95	7.87571e-007
Total log likelihood of joint reconstruction:							-3428.24

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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="cog3577" 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	1.80582e-012	24	1.69502e-013	48	2.75228e-024	72	1.85251e-024
1	2.92304e-005	25	7.84775e-020	49	2.10545e-010	73	1.02465e-015
2	3.79614e-006	26	1.62879e-017	50	0.076748	74	0.000720076
3	0.000626705	27	2.52304e-026	51	0.000626705	75	1.92368e-006
4	9.77922e-006	28	1.19596e-027	52	2.3771e-023	76	0.000626705
5	7.70666e-012	29	8.536e-025	53	1.73267e-012	77	3.09773e-011
6	5.08442e-018	30	4.10688e-018	54	2.67044e-029	78	2.28963e-010
7	1.81423e-009	31	1.74533e-021	55	4.44621e-019	79	1.20122e-011
8	2.65162e-010	32	3.79614e-006	56	1.85173e-023	80	1.39913e-006
9	2.48847e-010	33	9.77922e-006	57	1.98711e-018	81	2.69086e-023
10	2.77317e-014	34	1.09471e-009	58	9.38164e-010	82	3.96295e-019
11	8.09735e-028	35	0.000626705	59	1.70881e-025	83	3.40201e-009
12	3.68933e-022	36	3.39915e-029	60	3.24023e-009	84	8.62342e-022
13	1.42431e-021	37	5.09608e-018	61	1.21169e-005	85	5.31376e-014
14	2.11042e-007	38	4.58757e-020	62	3.41773e-019	86	5.48279e-018
15	5.01155e-023	39	1.1494e-011	63	1.68689e-010	87	4.21793e-024
16	5.37545e-018	40	2.75308e-015	64	2.40671e-021	88	5.31678e-019
17	5.63428e-012	41	1.14821e-017	65	5.26466e-011	89	2.65059e-018
18	2.42151e-007	42	4.18346e-013	66	4.62217e-019	90	1.21368e-024
19	1.50733e-015	43	5.65816e-025	67	5.47849e-012	91	1.08706e-011
20	8.5699e-020	44	1.14263e-013	68	2.15054e-013	92	5.33312e-027
21	3.48943e-024	45	2.66574e-019	69	1.87531e-026	93	1.93197e-012
22	2.73029e-021	46	8.77322e-024	70	8.64622e-012	94	2.97193e-018
23	2.03014e-019	47	3.13272e-012	71	1.02213e-018	95	8.18661e-007
Total log likelihood of joint reconstruction:							-3300.18

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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="cog3577" 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_cog3577 profile HMM generated consensus sequence
VDTGASsVaLneedArrLGldpssldytvtvsTANGqtrAArvtLdrvqiGgItlrdVd
AvVlkeGaqlsesLLGMSFLkrLesfevrggtLiL

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

        Domain 1 of 1, from 1 to 87: score 43.7, E = 7.2e-14

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    vDTGAs    +++e  +a +lg                     ++Ps
AP_cog3577     1    VDTGASS-VALNEE--DARRLG---------------------LDPS 23   

                 sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                 s + t +   + +a+Gq+++        ++         +++i  G++  
AP_cog3577    24 SLDYTVT---VSTANGQTRA------ARVTL-------DRVQI--GGI-- 53   

                 venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvhidl<-*
                   + + + d   +v+++  +      + +LG+  fL+ l+s  +++   
AP_cog3577    54 --TLRDV-D--AVVLkEGAQL----SESLLGM-SFLKRLES--FEV    87   

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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.