TraL - PFAM28P - GREMLIN Contacts

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TraL - TraL protein

PFAM:	PF07178	Sequences: YRIPRYLDDPPRILFWELDEAAPFLLPFFLGILLGQLLLGLILGLLLAFLYRKLKKGKGPGFLLHLLYWYLPSSLLRKLKATPPSHIREFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (88)
Sequences:	1688 (1310)
Seq/√Len:	139.6
META:	0.83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_D	55_K	4.144	1.00
20_E	52_R	3.427	1.00
58_K	62_F	3.289	1.00
79_L	82_T	2.346	1.00
3_I	8_D	2.174	1.00
6_Y	9_D	2.168	1.00
66_L	70_Y	2.158	1.00
17_E	55_K	2.141	1.00
36_Q	39_L	2.136	1.00
12_R	17_E	2.073	1.00
48_A	52_R	1.941	1.00
69_W	88_R	1.897	1.00
17_E	20_E	1.866	1.00
45_L	49_F	1.845	1.00
29_F	33_L	1.653	1.00
44_G	48_A	1.616	1.00
87_I	90_F	1.558	1.00
20_E	48_A	1.555	1.00
69_W	85_S	1.521	1.00
13_I	21_A	1.481	1.00
61_G	65_H	1.466	1.00
37_L	64_L	1.426	1.00
23_P	48_A	1.423	1.00
46_L	50_L	1.386	1.00
63_L	67_L	1.383	1.00
8_D	15_F	1.299	1.00
23_P	51_Y	1.288	1.00
62_F	65_H	1.249	1.00
84_P	87_I	1.211	1.00
23_P	27_P	1.206	1.00
40_G	44_G	1.178	1.00
46_L	49_F	1.164	0.99
27_P	40_G	1.156	0.99
9_D	17_E	1.144	0.99
12_R	20_E	1.115	0.99
24_F	48_A	1.114	0.99
67_L	71_L	1.092	0.99
27_P	31_G	1.077	0.99
62_F	66_L	1.070	0.99
24_F	44_G	1.055	0.99
4_P	56_K	1.027	0.99
16_W	21_A	0.996	0.98
28_F	41_L	0.971	0.98
56_K	61_G	0.967	0.98
7_L	68_Y	0.962	0.98
31_G	40_G	0.944	0.98
36_Q	40_G	0.936	0.98
85_S	88_R	0.929	0.97
27_P	47_L	0.921	0.97
74_S	81_A	0.898	0.97
19_D	51_Y	0.896	0.97
18_L	73_S	0.894	0.97
40_G	43_L	0.877	0.96
5_R	8_D	0.868	0.96
75_L	80_K	0.864	0.96
2_R	54_L	0.860	0.96
52_R	56_K	0.852	0.96
44_G	53_K	0.833	0.95
27_P	48_A	0.824	0.95
42_I	73_S	0.823	0.95
3_I	6_Y	0.813	0.94
13_I	18_L	0.810	0.94
2_R	42_I	0.808	0.94
83_P	90_F	0.808	0.94
9_D	16_W	0.807	0.94
50_L	54_L	0.793	0.94
26_L	74_S	0.777	0.93
40_G	50_L	0.775	0.93
4_P	7_L	0.766	0.93
24_F	27_P	0.761	0.92
15_F	62_F	0.759	0.92
34_L	46_L	0.742	0.91
11_P	17_E	0.740	0.91
68_Y	85_S	0.718	0.90
23_P	47_L	0.714	0.90
39_L	42_I	0.712	0.90
15_F	23_P	0.711	0.89
18_L	22_A	0.700	0.89
9_D	12_R	0.695	0.88
8_D	69_W	0.683	0.88
20_E	55_K	0.680	0.87
39_L	43_L	0.676	0.87
30_L	34_L	0.675	0.87
20_E	29_F	0.673	0.87
8_D	47_L	0.665	0.86
10_P	17_E	0.664	0.86
29_F	32_I	0.664	0.86
66_L	89_E	0.663	0.86
24_F	38_L	0.661	0.86
30_L	35_G	0.660	0.86
51_Y	66_L	0.654	0.85
68_Y	72_P	0.653	0.85
55_K	67_L	0.648	0.85
31_G	36_Q	0.633	0.83
26_L	45_L	0.629	0.83
62_F	68_Y	0.627	0.83
18_L	32_I	0.626	0.83
4_P	8_D	0.622	0.82
16_W	27_P	0.621	0.82
16_W	20_E	0.621	0.82
80_K	86_H	0.620	0.82
33_L	46_L	0.615	0.82
47_L	63_L	0.615	0.82
76_L	83_P	0.612	0.81
30_L	50_L	0.612	0.81
21_A	25_L	0.612	0.81
22_A	67_L	0.609	0.81
61_G	89_E	0.608	0.81
73_S	76_L	0.604	0.80
58_K	65_H	0.598	0.80
6_Y	12_R	0.594	0.79
5_R	60_P	0.591	0.79
21_A	73_S	0.591	0.79
28_F	66_L	0.584	0.78
47_L	50_L	0.582	0.78
79_L	90_F	0.577	0.77
9_D	28_F	0.569	0.76
57_G	64_L	0.569	0.76
27_P	41_L	0.566	0.76
9_D	70_Y	0.566	0.76
24_F	41_L	0.565	0.76
34_L	37_L	0.552	0.74
26_L	77_R	0.544	0.73
26_L	29_F	0.534	0.72
24_F	90_F	0.534	0.72
14_L	30_L	0.531	0.71
21_A	72_P	0.530	0.71
3_I	21_A	0.526	0.71
58_K	61_G	0.526	0.71
74_S	77_R	0.523	0.70
6_Y	17_E	0.502	0.67
24_F	37_L	0.500	0.67

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
3ixzA	1	0.7582	7.2	0.897	Contact Map
3j9tb	1	0	5.1	0.904	Contact Map
2zxeA	1	0.7582	5	0.904	Contact Map
2nr9A	2	0.6813	5	0.904	Contact Map
2ks1B	1	0.4835	4.2	0.908	Contact Map
4p02B	1	0.5055	2.4	0.918	Contact Map
4u2pA	4	0.4945	2.4	0.919	Contact Map
4tllA	1	0.3077	1.9	0.922	Contact Map
3kcuA	3	0.5495	1.8	0.924	Contact Map
2jwaA	2	0.4835	1.8	0.924	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.

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