LRGA - BACSU - GREMLIN Contacts

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LRGA - Antiholin-like protein LrgA

UniProt:	P94515	Sequences: MSAKKVYGFLTQAFIFAVIMLVSNMIAAIVPIPIPASVVGLVLLFLLLCLKVIKLEQVETLGTSLTSLIGFLFVPSGISVMNSLGVMQQYGLQIVLVILLATIILLGATGLFSQLILSLSGKRKTEADMKTKTVQSPQNNNELVHH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (116)
Sequences:	1784 (1351)
Seq/√Len:	125.4

ECOLI - YOHJ
BACSU - LRGA YXZK CIDA

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_I	47_L	4.592	1.00
46_L	50_L	3.107	1.00
108_A	112_F	2.778	1.00
111_L	114_Q	2.775	1.00
107_G	111_L	2.541	1.00
110_G	114_Q	2.316	1.00
27_A	39_V	2.296	1.00
42_V	46_L	2.266	1.00
81_M	84_L	1.992	1.00
22_V	47_L	1.911	1.00
19_I	43_L	1.843	1.00
18_V	22_V	1.825	1.00
93_Q	97_V	1.824	1.00
12_Q	61_L	1.807	1.00
54_K	57_Q	1.796	1.00
20_M	24_N	1.775	1.00
39_V	43_L	1.753	1.00
100_L	104_I	1.742	1.00
112_F	115_L	1.725	1.00
23_S	36_A	1.718	1.00
37_S	72_L	1.711	1.00
87_M	94_I	1.690	1.00
24_N	28_A	1.667	1.00
90_Y	93_Q	1.659	1.00
41_L	77_G	1.587	1.00
20_M	37_S	1.577	1.00
55_L	58_V	1.464	1.00
43_L	47_L	1.453	1.00
35_P	76_S	1.451	1.00
115_L	119_L	1.450	1.00
80_V	83_S	1.449	1.00
26_I	29_I	1.445	1.00
111_L	115_L	1.433	1.00
51_K	54_K	1.406	1.00
11_T	57_Q	1.390	1.00
25_M	29_I	1.362	1.00
41_L	113_S	1.277	1.00
85_G	88_Q	1.273	1.00
96_L	100_L	1.257	1.00
83_S	86_V	1.254	1.00
55_L	59_E	1.249	1.00
19_I	23_S	1.248	1.00
42_V	64_S	1.162	0.99
47_L	52_V	1.134	0.99
27_A	30_V	1.111	0.99
116_I	119_L	1.110	0.99
84_L	88_Q	1.110	0.99
115_L	118_S	1.101	0.99
16_F	61_L	1.096	0.99
11_T	14_F	1.096	0.99
105_L	109_T	1.079	0.99
113_S	117_L	1.074	0.99
119_L	122_K	1.070	0.99
67_S	76_S	1.068	0.99
85_G	89_Q	1.064	0.98
47_L	53_I	1.043	0.98
26_I	43_L	1.032	0.98
59_E	63_T	1.017	0.98
119_L	123_R	1.007	0.98
23_S	39_V	1.003	0.98
33_P	38_V	0.993	0.98
13_A	61_L	0.985	0.97
109_T	113_S	0.973	0.97
27_A	36_A	0.962	0.97
12_Q	19_I	0.955	0.97
24_N	36_A	0.952	0.97
22_V	121_G	0.946	0.97
41_L	58_V	0.945	0.97
26_I	39_V	0.940	0.97
27_A	31_P	0.928	0.96
17_A	79_S	0.922	0.96
86_V	90_Y	0.907	0.96
26_I	30_V	0.887	0.95
44_L	53_I	0.882	0.95
23_S	79_S	0.879	0.95
90_Y	94_I	0.868	0.95
38_V	70_G	0.841	0.94
26_I	31_P	0.836	0.94
15_I	18_V	0.830	0.93
25_M	28_A	0.830	0.93
26_I	59_E	0.828	0.93
120_S	123_R	0.814	0.93
58_V	66_T	0.811	0.93
13_A	23_S	0.803	0.92
13_A	101_A	0.801	0.92
66_T	69_I	0.797	0.92
82_N	85_G	0.795	0.92
49_C	52_V	0.783	0.91
47_L	50_L	0.776	0.91
98_I	105_L	0.774	0.91
37_S	45_F	0.767	0.90
38_V	83_S	0.765	0.90
42_V	45_F	0.764	0.90
78_I	81_M	0.763	0.90
81_M	99_L	0.762	0.90
103_I	107_G	0.748	0.89
70_G	74_V	0.740	0.89
8_G	60_T	0.738	0.89
17_A	109_T	0.735	0.88
11_T	15_I	0.733	0.88
102_T	105_L	0.725	0.88
18_V	115_L	0.722	0.88
20_M	35_P	0.718	0.87
46_L	112_F	0.714	0.87
45_F	49_C	0.706	0.86
73_F	76_S	0.705	0.86
23_S	41_L	0.701	0.86
53_I	57_Q	0.699	0.86
68_L	71_F	0.694	0.85
37_S	106_L	0.692	0.85
51_K	55_L	0.691	0.85
12_Q	64_S	0.683	0.85
109_T	117_L	0.680	0.84
55_L	90_Y	0.679	0.84
17_A	23_S	0.674	0.84
52_V	55_L	0.672	0.84
34_I	79_S	0.669	0.83
58_V	62_G	0.666	0.83
76_S	87_M	0.665	0.83
86_V	94_I	0.664	0.83
92_L	99_L	0.658	0.82
38_V	66_T	0.655	0.82
96_L	122_K	0.654	0.82
77_G	84_L	0.653	0.82
102_T	106_L	0.653	0.82
65_L	70_G	0.652	0.82
70_G	77_G	0.650	0.81
37_S	98_I	0.629	0.79
70_G	101_A	0.627	0.79
114_Q	119_L	0.626	0.79
11_T	56_E	0.622	0.79
36_A	39_V	0.622	0.79
98_I	102_T	0.621	0.78
113_S	116_I	0.621	0.78
40_G	58_V	0.612	0.77
22_V	43_L	0.610	0.77
97_V	106_L	0.606	0.77
37_S	66_T	0.605	0.77
88_Q	122_K	0.601	0.76
70_G	105_L	0.599	0.76
38_V	69_I	0.594	0.75
78_I	85_G	0.590	0.75
9_F	80_V	0.583	0.74
27_A	32_I	0.575	0.73
9_F	60_T	0.567	0.72
19_I	44_L	0.566	0.72
31_P	42_V	0.566	0.72
112_F	116_I	0.564	0.72
71_F	86_V	0.561	0.71
59_E	79_S	0.558	0.71
12_Q	60_T	0.556	0.71
64_S	69_I	0.550	0.70
53_I	69_I	0.548	0.69
71_F	74_V	0.538	0.68
77_G	83_S	0.537	0.68
12_Q	48_L	0.536	0.68
50_L	55_L	0.535	0.68
19_I	22_V	0.534	0.67
80_V	84_L	0.533	0.67
47_L	51_K	0.533	0.67
41_L	103_I	0.533	0.67
77_G	80_V	0.532	0.67
20_M	110_G	0.525	0.66
16_F	23_S	0.522	0.66
15_I	19_I	0.522	0.66
19_I	87_M	0.517	0.65
30_V	39_V	0.516	0.65
38_V	78_I	0.514	0.65
57_Q	61_L	0.508	0.64
70_G	93_Q	0.507	0.63
89_Q	100_L	0.503	0.63
69_I	74_V	0.503	0.63
12_Q	20_M	0.501	0.63
54_K	100_L	0.500	0.62

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
2kluA	1	0.411	61.7	0.91	Contact Map
3w9iA	3	0.8356	61.7	0.91	Contact Map
4mt1A	3	0.8082	59.9	0.911	Contact Map
4dx5A	3	0.8904	53.5	0.915	Contact Map
4cz8A	2	0.9521	46.8	0.918	Contact Map
4k0jA	3	0.7877	33.4	0.925	Contact Map
3aqpA	1	0.7877	29.7	0.927	Contact Map
2kncA	1	0.363	26.9	0.928	Contact Map
2m20A	2	0.3425	20.6	0.932	Contact Map
4czbA	2	0.9521	19.6	0.933	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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