CAARD:Spumaretroviridae

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

(EFV:0.238833,(FFV:0.023485,FSV:0.042109)N2:0.306572,(HFV:0.234101,SFV:0.140934)N3:0.179964);

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Fin output: Parental relationship among reconstructed nodes and OTUs

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Name	Father	Distance to father	Sons
EFV	N1	0.238833	-
FFV	N2	0.0234848	-
FSV	N2	0.0421088	-
HFV	N3	0.234101	-
SFV	N3	0.140934	-
N1	root!	-	EFV N2 N3
N2	N1	0.306572	FFV FSV
N3	N1	0.179964	HFV SFV

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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	5.38165e-005	36	0.0163904	72	0.000609575	108	0.0192524
1	0.0157724	37	0.0159724	73	5.80535e-007	109	9.28822e-009
2	0.000941077	38	0.0159724	74	8.01854e-005	110	0.0210204
3	0.000154035	39	4.50382e-005	75	0.0427951	111	0.0159724
4	0.0185706	40	0.000449852	76	0.000483347	112	8.46963e-006
5	8.28536e-006	41	0.00135471	77	0.0427951	113	1.69495e-006
6	0.000341814	42	0.0210204	78	0.0127656	114	0.0427951
7	0.0127656	43	0.00191487	79	0.00026707	115	0.00990647
8	0.0102574	44	6.82761e-006	80	6.8191e-005	116	0.0122447
9	0.00197487	45	0.0346535	81	0.000120462	117	1.32629e-006
10	0.0219636	46	0.0160012	82	3.26162e-005	118	0.00990647
11	4.30465e-007	47	0.00210299	83	2.17262e-006	119	0.0212073
12	3.19192e-009	48	0.000119588	84	0.0007896	120	0.00982481
13	0.00135471	49	5.3135e-006	85	0.000563605	121	0.0122447
14	0.0427951	50	0.00163053	86	2.81052e-005	122	0.0163904
15	1.96977e-006	51	0.0212073	87	0.000350486	123	0.0346535
16	6.0325e-005	52	0.0163904	88	1.95868e-006	124	0.00617817
17	0.0212073	53	0.0128442	89	6.54418e-007	125	0.0160012
18	2.92775e-006	54	4.60951e-005	90	0.0012468	126	2.30157e-005
19	0.0219636	55	0.00074352	91	0.0427951	127	0.0128442
20	0.0025148	56	8.0892e-006	92	4.06985e-007	128	9.23027e-006
21	3.00009e-005	57	7.76743e-005	93	2.0497e-007	129	0.0219636
22	3.25698e-007	58	0.00176538	94	0.0013369	130	0.00617817
23	8.88376e-008	59	0.0159724	95	2.83628e-008	131	4.70692e-006
24	3.83208e-009	60	0.000108371	96	0.0427951	132	0.0128442
25	0.0025148	61	0.000674823	97	2.07178e-005	133	0.0185706
26	1.20134e-005	62	6.75141e-005	98	1.34233e-007	134	0.0127656
27	0.0127656	63	9.33133e-005	99	3.39411e-007	135	0.0346535
28	0.0128442	64	0.0219636	100	1.00373e-007	136	8.58916e-005
29	0.00617817	65	5.27655e-005	101	0.0210204	137	1.33635e-006
30	0.0346535	66	0.0157724	102	1.747e-005	138	2.20555e-006
31	2.36026e-006	67	0.000374918	103	5.68067e-008	139	0.0219636
32	1.218e-005	68	0.0219636	104	0.0427951	140	2.08666e-005
33	1.747e-005	69	0.00990647	105	0.000360498	141	0.0219636
34	9.93251e-007	70	3.99612e-006	106	5.89657e-010
35	6.67866e-008	71	2.61721e-007	107	0.0427951
Total log likelihood of joint reconstruction:							-1170.16

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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="spumaretroviridae" 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	5.39429e-005	36	0.0164673	72	0.000624667	108	0.0192564
1	0.0158022	37	0.0159757	73	6.8528e-007	109	3.001e-008
2	0.00103337	38	0.0159757	74	8.133e-005	110	0.0210437
3	0.000155907	39	6.85118e-005	75	0.0428175	111	0.0159757
4	0.0186019	40	0.0004647	76	0.000536886	112	1.14869e-005
5	1.94975e-005	41	0.00137545	77	0.0428175	113	3.46889e-006
6	0.000376027	42	0.0210437	78	0.0127835	114	0.0428175
7	0.0127835	43	0.00205224	79	0.000282481	115	0.00990647
8	0.0102575	44	7.26115e-006	80	7.16352e-005	116	0.0122492
9	0.00215097	45	0.0346585	81	0.000291131	117	4.0908e-006
10	0.0219664	46	0.016018	82	3.41474e-005	118	0.00990647
11	1.23857e-006	47	0.00222136	83	2.33433e-006	119	0.0212479
12	5.93373e-009	48	0.000248522	84	0.000806841	120	0.00983248
13	0.00137545	49	1.31476e-005	85	0.000582907	121	0.0122492
14	0.0428175	50	0.00172856	86	3.01171e-005	122	0.0164673
15	3.31103e-006	51	0.0212479	87	0.000366387	123	0.0346585
16	6.95011e-005	52	0.0164673	88	2.45704e-006	124	0.00617957
17	0.0212479	53	0.0128941	89	2.26225e-006	125	0.016018
18	4.55511e-006	54	9.71756e-005	90	0.0012795	126	2.60973e-005
19	0.0219664	55	0.000889906	91	0.0428175	127	0.0128941
20	0.00272774	56	1.28445e-005	92	7.16817e-007	128	1.3172e-005
21	4.91919e-005	57	8.27521e-005	93	9.80248e-007	129	0.0219664
22	1.71897e-006	58	0.0018584	94	0.00140047	130	0.00617957
23	3.20357e-007	59	0.0159757	95	1.14778e-007	131	8.52544e-006
24	1.89377e-008	60	0.000163348	96	0.0428175	132	0.0128941
25	0.00272774	61	0.000765705	97	4.23819e-005	133	0.0186019
26	1.93766e-005	62	0.000161294	98	5.76599e-007	134	0.0127835
27	0.0127835	63	0.000244769	99	9.28581e-007	135	0.0346585
28	0.0128941	64	0.0219664	100	3.34824e-007	136	8.75251e-005
29	0.00617957	65	5.81919e-005	101	0.0210437	137	1.58573e-006
30	0.0346585	66	0.0158022	102	2.02749e-005	138	2.36759e-006
31	4.91344e-006	67	0.000571642	103	1.28046e-007	139	0.0219664
32	1.87707e-005	68	0.0219664	104	0.0428175	140	4.7806e-005
33	2.02749e-005	69	0.00990647	105	0.000383944	141	0.0219664
34	1.18159e-006	70	7.50055e-006	106	5.32244e-009
35	1.16635e-007	71	3.9184e-007	107	0.0428175
Total log likelihood of joint reconstruction:							-1130.91

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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="spumaretroviridae" 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_spumaretroviridae profile HMM generated consensus sequence
wDsgAditCvPksfLeeEePikkrliktiHGekeenvYYltfKiqGRkveaEvigtpld
YvlisPsDiPWllkkpLeLtikvdlqeqqerlLnktiLskegKeqLksLFvKYdnLWqh
WEnqvGHRrirPHkiAtGtvnPrP

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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 36.8, E = 8.6e-12

DTG_ILG template *->vDTGAsvlsviskecklaqklgltrkkafdpSSYvCivtllsysqPs
                    +D+GA++ ++++k+   ++                          P+
AP_spumare     1    WDSGADI-TCVPKS--FLEEEE-----------------------PI 21   

                 sktsttaqdtirgagGqs..kiyvSklktsgqirknllslvtikitkGnv
                 +k+       i++++G++++++y+  l++++q rk     v+ ++  G  
AP_spumare    22 KKRL------IKTIHGEKeeNVYY--LTFKIQGRK-----VEAEVI-G-- 55   

                 TevenrslpsdgvflvvtdpedqksrydvILGrldfLrqlnsvhidl<-*
                       +++ d   +++ +p+d    ++++L   ++    +   +dl   
AP_spumare    56 ------TPL-D--YVLI-SPSD----IPWLLKK-PLELTIK---VDL    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.