CAARD:Deltaretroviridae

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

(STcLV2PP:0.173401,HTLV-2:0.201136,(HTLV-1:0.276098,BLV:0.665907)N2:0.028256);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
STcLV2PP	N1	0.173401	-
HTLV-2	N1	0.201136	-
HTLV-1	N2	0.276098	-
BLV	N2	0.665907	-
N1	root!	-	STcLV2PP HTLV-2 N2
N2	N1	0.028256	HTLV-1 BLV

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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	0.00335036	25	0.0177157	50	0.0592915	75	0.000562148
1	0.0136762	26	1.11403e-005	51	0.0344702	76	0.00937192
2	0.0105441	27	0.0037952	52	0.0592915	77	2.46199e-005
3	0.0311957	28	0.000275664	53	1.32125e-008	78	0.01097
4	0.0156187	29	0.0790284	54	1.90757e-005	79	0.00222891
5	0.00437991	30	0.00145989	55	1.879e-008	80	0.0311957
6	7.34474e-006	31	0.038708	56	0.000320615	81	0.0137505
7	0.0105441	32	0.0311957	57	0.0194846	82	0.0136762
8	0.0140964	33	0.0156187	58	0.0173713	83	1.26944e-005
9	0.000966719	34	0.000838808	59	0.00020567	84	0.038708
10	0.0194846	35	0.0311957	60	1.13199e-005	85	0.000445848
11	2.70168e-005	36	0.000199454	61	5.07906e-006	86	4.18938e-005
12	3.60608e-005	37	0.00254954	62	0.0194846	87	0.000204005
13	0.0588794	38	2.78071e-007	63	3.03271e-005	88	0.0103743
14	2.22703e-008	39	1.14145e-006	64	4.9756e-005	89	6.52163e-005
15	0.00182765	40	5.07464e-005	65	0.038708	90	2.40935e-005
16	6.51069e-007	41	0.00201139	66	6.00089e-005	91	0.00328935
17	0.0306601	42	0.00134702	67	0.0263603	92	0.000466942
18	0.000767098	43	0.000236969	68	0.0135013	93	0.00328935
19	0.000128123	44	0.000231898	69	0.0588794	94	0.0194846
20	3.79375e-006	45	0.000133794	70	0.000537525	95	0.00146246
21	0.000641099	46	1.7857e-006	71	0.0136762	96	8.80624e-005
22	1.16823e-005	47	0.0194846	72	0.0105441
23	1.7178e-006	48	0.00131973	73	5.26516e-008
24	0.0790284	49	0.0246673	74	9.94145e-005
Total log likelihood of joint reconstruction:							-710.58

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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="deltaretroviridae" 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	0.00336122	25	0.022944	50	0.091904	75	0.000569197
1	0.013687	26	1.39118e-005	51	0.076748	76	0.00937192
2	0.0105502	27	0.00391318	52	0.091904	77	2.71428e-005
3	0.0311973	28	0.000318086	53	2.23671e-008	78	0.0109891
4	0.0156298	29	0.091904	54	2.41384e-005	79	0.00224288
5	0.00441295	30	0.00157341	55	3.73566e-008	80	0.0311973
6	9.14812e-006	31	0.0387159	56	0.000321391	81	0.0137565
7	0.0105502	32	0.0311973	57	0.0194854	82	0.013687
8	0.0141274	33	0.0156298	58	0.0173727	83	1.77888e-005
9	0.000979429	34	0.000843902	59	0.000206124	84	0.0387159
10	0.0194854	35	0.0311973	60	1.99805e-005	85	0.000446589
11	2.71847e-005	36	0.000199738	61	1.15331e-005	86	4.66366e-005
12	4.38057e-005	37	0.002563	62	0.0194854	87	0.000204057
13	0.0589482	38	9.33953e-007	63	3.70333e-005	88	0.0103758
14	4.10492e-008	39	3.80209e-006	64	5.97147e-005	89	7.09177e-005
15	0.0032753	40	5.84148e-005	65	0.0387159	90	2.57568e-005
16	1.1079e-006	41	0.00201793	66	0.000118587	91	0.00330082
17	0.066005	42	0.0013504	67	0.0264607	92	0.000467389
18	0.00123554	43	0.000237292	68	0.0135029	93	0.00330082
19	0.000207749	44	0.000235106	69	0.0589482	94	0.0194854
20	8.96983e-006	45	0.000134645	70	0.000548147	95	0.00152761
21	0.000646159	46	2.35203e-006	71	0.013687	96	9.68826e-005
22	1.44494e-005	47	0.0194854	72	0.0105502
23	1.83724e-006	48	0.00134214	73	1.41382e-007
24	0.091904	49	0.058565	74	0.000102332
Total log likelihood of joint reconstruction:							-693.255

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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="deltaretroviridae" 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_deltaretroviridae profile HMM generated consensus sequence [hmmemit]
lDTGAdlTVLPqaLvpsvedvPvkdttVLGAGGqtrnqFkllqsPLtlalkielPFrtt
PviLsSCLVDTknkWaIiGRDvLqqcQgvlylPed

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

         domain 1 of 1, from 1 to 90: score 42.3, E = 1.8e-13

  DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                      +DTGA++ +v+++   l+                         + P 
  AP_deltare     1    LDTGADL-TVLPQA--LVPSVE---------------------DVPV 23   

                   sktsttaqdtirgagGqs..kiyvSklktsgqirknllslvtikitkGnv
                   ++t+      + gagGq++++       ++ q++  l+++++i++     
  AP_deltare    24 KDTT------VLGAGGQTrnQF------KLLQSP--LTLALKIEL--P-- 55   

                   Tevenrslpsdgvflvv.tdpedqks.rydvILGrldfLrqlnsvhidl<-*
                          + ++  +++++ +++d +++++ +I+Gr d+L+q+++  + + 
  AP_deltare    56 -------FRTT--PVILsSCLVD-TKnKW-AIIGR-DVLQQCQG--VLY  90   

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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.