CAARD:Caulimoviridae

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

(BRRV:0.363223,((CVMV:0.637591,(RTBV:0.881718,((TBV:0.539049,(CYMV:0.184009,CSSV:0.236844)N7:0.042530)N6:0.084530,(SBV:0.444779, (KTSV:0.230851,BSV:0.288366)N9:0.180600)N8:0.042234)N5:0.312026)N4:0.152466)N3:0.176768,(SVBV:0.384832,(CaMV:0.202691,(CERV:0.300086, (MMV:0.228200,(FMV:0.134410,DMV:0.131026)N14:0.079850)N13:0.050147)N12:0.029419)N11:0.043424)N10:0.147755)N2:0.160175,(SbCMV:0.402013, (PCSV:0.371774,CYLCV:0.350015)N16:0.032916)N15:0.018833);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
BRRV	N1	0.363223	-
CVMV	N3	0.637591	-
RTBV	N4	0.881718	-
TBV	N6	0.539049	-
CYMV	N7	0.184009	-
CSSV	N7	0.236844	-
SBV	N8	0.444779	-
KTSV	N9	0.230851	-
BSV	N9	0.288366	-
SVBV	N10	0.384832	-
CaMV	N11	0.202691	-
CERV	N12	0.300086	-
MMV	N13	0.2282	-
FMV	N14	0.13441	-
DMV	N14	0.131026	-
SbCMV	N15	0.402013	-
PCSV	N16	0.371774	-
CYLCV	N16	0.350015	-
N1	root!	-	BRRV N2 N15
N2	N1	0.160175	N3 N10
N3	N2	0.176768	CVMV N4
N4	N3	0.152466	RTBV N5
N5	N4	0.312026	N6 N8
N6	N5	0.0845304	TBV N7
N7	N6	0.0425305	CYMV CSSV
N8	N5	0.0422345	SBV N9
N9	N8	0.1806	KTSV BSV
N10	N2	0.147755	SVBV N11
N11	N10	0.0434235	CaMV N12
N12	N11	0.0294185	CERV N13
N13	N12	0.0501468	MMV N14
N14	N13	0.07985	FMV DMV
N15	N1	0.0188328	SbCMV N16
N16	N15	0.0329159	PCSV CYLCV

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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	7.29263e-011	32	2.97321e-014	64	7.34051e-017	96	0.000296046
1	2.08886e-005	33	3.58782e-013	65	6.92923e-020	97	7.00137e-015
2	8.03596e-007	34	1.17773e-026	66	1.76561e-020	98	1.53441e-010
3	0.000494463	35	3.15967e-013	67	2.84189e-028	99	1.2218e-017
4	1.39289e-007	36	2.35722e-019	68	2.76896e-005	100	6.51548e-014
5	2.27823e-011	37	5.58372e-011	69	4.12527e-027	101	2.1351e-012
6	1.49912e-017	38	0.000115678	70	6.42354e-012	102	3.95936e-019
7	0.00022636	39	1.53633e-010	71	0.00719497	103	0.0024444
8	5.77138e-006	40	1.62056e-011	72	0.00758651	104	0.00300215
9	7.07139e-015	41	4.45526e-019	73	0.0024444	105	0.00262271
10	5.38338e-019	42	0.000253743	74	0.019163	106	0.00300215
11	1.6775e-022	43	2.56186e-025	75	3.91079e-007	107	0.00152142
12	1.56167e-012	44	3.46782e-027	76	1.58051e-019	108	0.00719497
13	9.41236e-016	45	4.32692e-024	77	1.70366e-008	109	0.00464171
14	1.0096e-020	46	2.51807e-025	78	2.01149e-014	110	1.70753e-008
15	2.60008e-014	47	3.57657e-022	79	1.86842e-016	111	1.36581e-012
16	2.82417e-011	48	3.72296e-023	80	1.02466e-011	112	7.12848e-007
17	1.88843e-018	49	2.05744e-018	81	6.74726e-008	113	8.24521e-014
18	1.02598e-016	50	3.68767e-017	82	1.6437e-005	114	4.51991e-008
19	1.41563e-011	51	9.92609e-017	83	4.43852e-018	115	3.79039e-021
20	4.92493e-007	52	1.18994e-011	84	5.38862e-021	116	1.39614e-016
21	4.69162e-027	53	1.55043e-027	85	1.78583e-019	117	1.28258e-022
22	0.00223868	54	3.52359e-015	86	1.68585e-011	118	3.72019e-020
23	2.19534e-011	55	4.9967e-023	87	1.78766e-010	119	0.00378599
24	3.25178e-016	56	5.39737e-006	88	2.24791e-018	120	1.9553e-010
25	1.84511e-007	57	2.31023e-014	89	9.28698e-018	121	1.90183e-018
26	0.000389014	58	5.03191e-034	90	6.16295e-021	122	2.39151e-008
27	2.57658e-026	59	7.33408e-013	91	7.92811e-011	123	4.02254e-013
28	2.07038e-015	60	0.0034186	92	3.46343e-013	124	4.89559e-016
29	2.08338e-013	61	0.00880089	93	0.000494463	125	1.5219e-023
30	8.49017e-011	62	0.00719497	94	2.84725e-013	126	7.17307e-022
31	1.54163e-012	63	0.00701351	95	2.09331e-008	127	9.47549e-012
Total log likelihood of joint reconstruction:							-3706.46

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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="caulimoviridae" folder="jrof"></align>

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Mpf output: Marginal probability per amino acid position and total Log Likelihood

<tbody>

Position	Joint probability	Position	Joint probability	Position	Joint probability	Position	Joint probability
0	2.24686e-010	32	6.60519e-013	64	5.178e-016	96	0.00029637
1	2.11068e-005	33	1.14485e-012	65	5.24355e-019	97	3.53869e-014
2	8.26475e-007	34	3.98971e-025	66	7.12634e-020	98	1.46028e-009
3	0.000494827	35	7.53204e-013	67	1.84336e-027	99	9.29422e-017
4	1.44025e-007	36	4.31719e-019	68	2.77707e-005	100	1.66008e-013
5	3.57387e-011	37	9.38688e-011	69	5.10582e-026	101	1.13323e-011
6	2.04533e-016	38	0.000924235	70	2.12919e-011	102	3.31153e-018
7	0.000621205	39	7.46959e-010	71	0.058676	103	0.068765
8	5.78327e-006	40	3.77395e-011	72	0.032102	104	0.053761
9	1.50239e-014	41	1.00036e-017	73	0.068765	105	0.058565
10	7.99407e-018	42	0.0027651	74	0.091904	106	0.053761
11	9.66623e-022	43	6.87009e-024	75	3.95952e-007	107	0.022944
12	1.37372e-011	44	8.43915e-026	76	1.12859e-018	108	0.058676
13	1.83124e-015	45	1.42096e-022	77	7.29653e-008	109	0.051544
14	3.69497e-020	46	6.08814e-024	78	5.42501e-014	110	3.59132e-008
15	1.04341e-013	47	3.25807e-021	79	9.71813e-016	111	1.00523e-011
16	2.95014e-011	48	4.37383e-022	80	6.28351e-011	112	4.91441e-006
17	1.68511e-017	49	7.62289e-018	81	1.46962e-007	113	1.03763e-013
18	1.11897e-015	50	3.41581e-016	82	0.000112293	114	7.57141e-008
19	4.50512e-010	51	5.53589e-016	83	2.69454e-017	115	2.4569e-019
20	2.40285e-006	52	2.31814e-010	84	1.28873e-020	116	9.05718e-016
21	3.62092e-025	53	2.24395e-026	85	5.18683e-018	117	3.8267e-021
22	0.00827945	54	5.17243e-014	86	9.12423e-011	118	1.33308e-019
23	3.65651e-011	55	2.16515e-022	87	1.80825e-010	119	0.053761
24	1.88297e-014	56	5.83295e-005	88	2.63726e-017	120	8.92577e-010
25	2.92338e-007	57	8.26904e-014	89	2.7358e-017	121	4.45872e-018
26	0.00638423	58	9.2202e-032	90	8.79648e-020	122	2.52176e-008
27	2.21044e-024	59	1.80081e-012	91	1.01543e-010	123	6.10079e-013
28	2.67111e-015	60	0.040752	92	6.02062e-013	124	2.28424e-015
29	3.42442e-012	61	0.040126	93	0.000494827	125	9.74988e-023
30	1.00294e-009	62	0.058676	94	7.6988e-013	126	1.18715e-020
31	5.11742e-011	63	0.06183	95	2.1933e-008	127	2.20721e-010
Total log likelihood of joint reconstruction:							-3476.31

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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="caulimoviridae" 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_caulimoviruses profile HMM generated consensus sequence
iDTGAtlCiasekivpkewkenkekpikirianssvivirkvkkdgklwIadekFlIPt
tYPmqqesGidmIIGnNFlrslygpfrIqygdtItF

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

           Domain 1 of 1, from 1 to 89: score 63.1, E = 1e-19

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA++ +++s+   ++ k ++++k                 ++P+
  AP_caulimo     1    IDTGATL-CIASEK--IVPKEWKENK-----------------EKPI 27   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                    k        ir+a+           +++ i        ++k + G    
  AP_caulimo    28 -K--------IRIANS----------SVIVI-------RKVKKD-G---- 46   

                   venrslpsdgvflvv.tdpedqksrydvILGrldfLrqlnsvh.idl<-*
                     + ++++++ fl+++t p++q+s++d+I+G+  fLr l+++++i++   
  AP_caulimo    47 --KLWIADEK-FLIPtTYPMQQESGIDMIIGN-NFLRSLYGPFrIQY    89   

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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.