CtnDOT_TraJ - PFAM28P - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

CtnDOT_TraJ - Homologues of TraJ from Bacteroides conjugative transposon

PFAM:	PF07863	Sequences: FMIIGIVGYFTVPSVANYIVHAGGGGALLRKVTSLASSAGSSAGSAAGAGAGMAADAMGNAASRMS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (60)
Sequences:	1087 (735)
Seq/√Len:	94.8
META:	0.853

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_M	56_D	3.510	1.00
26_G	29_L	3.304	1.00
27_A	30_R	2.560	1.00
18_Y	22_A	2.111	1.00
56_D	60_N	1.941	1.00
57_A	60_N	1.927	1.00
47_A	50_G	1.890	1.00
18_Y	21_H	1.823	1.00
33_T	36_A	1.763	1.00
54_A	57_A	1.714	1.00
43_A	46_A	1.685	1.00
7_V	31_K	1.619	1.00
52_G	58_M	1.531	1.00
2_M	11_T	1.484	1.00
18_Y	28_L	1.472	1.00
18_Y	26_G	1.384	0.99
31_K	35_L	1.368	0.99
40_G	43_A	1.354	0.99
27_A	31_K	1.310	0.99
14_S	22_A	1.261	0.99
44_G	47_A	1.206	0.98
15_V	22_A	1.194	0.98
53_M	60_N	1.165	0.98
17_N	21_H	1.147	0.98
30_R	34_S	1.101	0.97
16_A	20_V	1.079	0.97
55_A	58_M	1.075	0.96
26_G	30_R	1.060	0.96
52_G	55_A	1.040	0.96
42_S	45_S	1.024	0.95
16_A	19_I	0.965	0.94
53_M	57_A	0.947	0.93
51_A	55_A	0.945	0.93
2_M	17_N	0.937	0.93
37_S	40_G	0.932	0.92
24_G	29_L	0.922	0.92
2_M	35_L	0.915	0.92
52_G	57_A	0.875	0.90
48_G	51_A	0.868	0.89
36_A	39_A	0.861	0.89
7_V	21_H	0.859	0.89
19_I	23_G	0.847	0.88
29_L	32_V	0.842	0.88
9_Y	16_A	0.814	0.86
50_G	54_A	0.807	0.86
44_G	48_G	0.800	0.85
11_T	19_I	0.796	0.85
28_L	31_K	0.795	0.85
5_G	14_S	0.795	0.85
48_G	54_A	0.779	0.84
10_F	33_T	0.760	0.82
15_V	18_Y	0.751	0.81
22_A	30_R	0.746	0.81
25_G	31_K	0.708	0.77
25_G	28_L	0.705	0.77
40_G	44_G	0.701	0.77
21_H	44_G	0.699	0.77
14_S	20_V	0.692	0.76
41_S	45_S	0.678	0.74
29_L	35_L	0.673	0.74
11_T	27_A	0.668	0.73
35_L	39_A	0.667	0.73
37_S	41_S	0.665	0.73
12_V	15_V	0.661	0.73
8_G	15_V	0.653	0.72
29_L	37_S	0.645	0.71
5_G	10_F	0.644	0.71
16_A	28_L	0.627	0.69
35_L	38_S	0.620	0.68
2_M	8_G	0.613	0.67
34_S	37_S	0.606	0.66
5_G	36_A	0.602	0.65
55_A	59_G	0.596	0.65
22_A	34_S	0.594	0.64
7_V	14_S	0.592	0.64
18_Y	27_A	0.588	0.64
16_A	42_S	0.572	0.61
16_A	37_S	0.570	0.61
2_M	55_A	0.563	0.60
3_I	7_V	0.547	0.58
11_T	28_L	0.544	0.58
14_S	26_G	0.542	0.57
12_V	28_L	0.531	0.56
7_V	35_L	0.522	0.55
54_A	58_M	0.517	0.54
48_G	52_G	0.514	0.54
17_N	25_G	0.510	0.53
47_A	52_G	0.508	0.53
32_V	36_A	0.506	0.52
18_Y	31_K	0.500	0.52

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3mp7B	1	0.3182	24.7	0.85	Contact Map
4w252	1	0.3333	14.2	0.866	Contact Map
2ww9B	1	0.3485	7	0.883	Contact Map
1ciiA	1	0.4697	7	0.884	Contact Map
1rh5B	1	0.3485	6.7	0.884	Contact Map
3hzqA	3	0.3333	6.3	0.885	Contact Map
1colA	1	0.5	2.7	0.904	Contact Map
3fewX	1	0.5455	1.5	0.917	Contact Map
1y43A	1	0.2727	1.5	0.917	Contact Map
1tpxA	1	0.2273	1.3	0.92	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

Page generated in 0.0044 seconds.