CAARD:Betaretroviridae

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

Top

Pin output : Ancestral tree

((SERV:0.083916,(MPMV:0.005850,SRV-1:0.005850)N3:0.086036)N2:0.183677, (MMTV:0.485878,(RTVL-H3:0.724208,HERV-K10:0.488442)N5:0.110959)N4:0.060627,(SMRV-H:0.239491,JSRV:0.359773)N6:0.031609);

Top

Fin output: Parental relationship among reconstructed nodes and OTUs

Show/Hide

Name	Father	Distance to father	Sons
SERV	N2	0.0839156	-
MPMV	N3	0.00584983	-
SRV-1	N3	0.00584983	-
MMTV	N4	0.485878	-
RTVL-H3	N5	0.724208	-
HERV-K10	N5	0.488442	-
SMRV-H	N6	0.239491	-
JSRV	N6	0.359773	-
N1	root!	-	N2 N4 N6
N2	N1	0.183677	SERV N3
N3	N2	0.0860362	MPMV SRV-1
N4	N1	0.0606267	MMTV N5
N5	N4	0.110959	RTVL-H3 HERV-K10
N6	N1	0.0316087	SMRV-H JSRV

Top

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	1.71239e-006	23	2.37951e-006	46	1.53929e-008	69	3.06092e-006
1	0.00304456	24	6.65944e-009	47	0.0115193	70	3.31159e-006
2	0.00151293	25	3.25017e-005	48	0.000135832	71	0.0145443
3	0.0118904	26	2.814e-010	49	1.97911e-011	72	0.000202726
4	0.00257428	27	0.001378	50	1.85621e-007	73	0.0118904
5	0.000109893	28	1.30865e-008	51	2.01843e-010	74	0.00307066
6	1.41809e-009	29	0.0118904	52	1.39693e-006	75	0.000469603
7	8.65925e-006	30	0.000246553	53	2.77061e-009	76	1.19715e-005
8	4.01624e-008	31	0.015944	54	1.19421e-008	77	0.000613426
9	0.000410954	32	0.0118904	55	7.98552e-006	78	1.72681e-007
10	4.28268e-008	33	3.42962e-007	56	0.000333466	79	6.16299e-007
11	1.29917e-014	34	1.27089e-005	57	1.45847e-010	80	1.21593e-007
12	5.30984e-011	35	6.63916e-009	58	1.74301e-008	81	4.91465e-008
13	9.63425e-010	36	3.4956e-007	59	5.86821e-008	82	0.00017905
14	0.000170846	37	0.0123011	60	0.0135052	83	5.21427e-008
15	0.00657246	38	1.20254e-006	61	7.16586e-005	84	9.36887e-006
16	1.05064e-011	39	2.96432e-009	62	5.03373e-008	85	9.09886e-007
17	1.39281e-007	40	1.3197e-005	63	4.85524e-006	86	2.67906e-005
18	0.000202726	41	7.34695e-005	64	3.03363e-005	87	3.42796e-011
19	0.000742579	42	2.07106e-007	65	0.000266521	88	3.05605e-015
20	1.86975e-012	43	1.11753e-008	66	2.00038e-010	89	2.30648e-012
21	1.6247e-008	44	3.86644e-011	67	5.01929e-006
22	3.78952e-011	45	0.0145443	68	0.00657246
Total log likelihood of joint reconstruction:							-1231.29

Top

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

Top

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	4.80258e-006	23	6.19938e-006	46	5.3106e-008	69	6.55895e-006
1	0.00305919	24	1.19586e-008	47	0.019803	70	3.52991e-006
2	0.0015189	25	3.35436e-005	48	0.000136001	71	0.0145634
3	0.0118946	26	1.29281e-009	49	7.76362e-011	72	0.000202842
4	0.00258627	27	0.00140306	50	2.53036e-007	73	0.0118946
5	0.000112604	28	2.95329e-008	51	5.79879e-010	74	0.0030792
6	1.7481e-009	29	0.0118946	52	2.21796e-006	75	0.000480443
7	1.68596e-005	30	0.000251009	53	1.40242e-008	76	1.33051e-005
8	1.10503e-007	31	0.051544	54	1.77564e-008	77	0.00061957
9	0.000425625	32	0.0118946	55	9.18254e-006	78	3.00394e-007
10	1.11153e-007	33	3.58359e-007	56	0.000453486	79	6.39003e-007
11	3.0013e-013	34	1.39955e-005	57	6.38798e-010	80	1.95249e-007
12	1.33671e-010	35	1.70167e-008	58	2.7485e-008	81	1.04134e-007
13	3.91664e-009	36	6.38944e-007	59	1.17943e-007	82	0.000645016
14	0.000170955	37	1	60	0.068765	83	7.92491e-007
15	0.00657451	38	1.35694e-006	61	7.22384e-005	84	2.38657e-005
16	5.43591e-011	39	8.51044e-009	62	1.66824e-007	85	5.63591e-006
17	1.4724e-007	40	1.34171e-005	63	8.81887e-006	86	7.08554e-005
18	0.000202842	41	7.61922e-005	64	5.56483e-005	87	6.22788e-011
19	0.000748945	42	3.91918e-007	65	0.00027154	88	2.54817e-014
20	7.64614e-012	43	1.28463e-008	66	5.82461e-010	89	3.63151e-012
21	4.05446e-008	44	8.27136e-011	67	6.64935e-006
22	2.91652e-010	45	0.0145634	68	0.00657451
Total log likelihood of joint reconstruction:							-1172.67

Top

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="betaretroviridae" folder="mrof"></align>

Top

Models

Sequence Logo

Error creating thumbnail: Unable to save thumbnail to destination

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.

Top

HMMs

>betaretroviridae profile HMM generated consensus sequence
lDTGADvtvIsskqWPtnWPiqktvThLrGIGqAsnPqqSsqlLtWrdkeqnSglikPf
ViPtLPlNLWGRDILsqmkismmslvm

Top

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

         Domain 1 of 1, from 1 to 84: score 42.8, E = 1.3e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA+v +vis    ++ +                        +P+
  AP_betaret     1    LDTGADV-TVISSK--QWPT-----------------------NWPI 21   

                   sktsttaqdtirgagGqskiyvSklktsgqirknllslvtikitkGnvTe
                   +kt t     +rg+ Gq ++       + q+ + ll++   + ++G    
  AP_betaret    22 QKTVTH----LRGI-GQ-AS------NPQQSSQ-LLTWRDKEQNSG---- 54   

                   venrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                        l     ++v++ +      +  ++Gr d+L+q++ +++ l   
  AP_betaret    55 -----LIK---PFVIPTL------PLNLWGR-DILSQMKISMMSL    84   

Top

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.