RIBL - HALSA - GREMLIN Contacts

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RIBL - FAD synthase

UniProt:	Q9HRB2	Sequences: MTRVVAQGTFDLIHPGHVHYLEDAAAMGDELHVILARRENVTHKDPPVLPNRQRRDVVAALDPVDHARIGHPEDIFAPIEAIDPDVIALGFDQHHDAAAIEAELADRGLDCAVERASPREARYDDEVLSSGDIADRVLAQRGDSDP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (127)
Sequences:	3057 (1854)
Seq/√Len:	164.5

ECOLI - HLDE
BACSU - TAGD
HALSA - RIBL
SULSO - Q97ZG4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_V	28_G	3.957	1.00
51_N	69_I	3.011	1.00
43_H	73_E	2.614	1.00
25_A	65_D	2.457	1.00
9_T	41_V	2.369	1.00
19_H	56_D	2.345	1.00
53_Q	128_L	2.219	1.00
77_A	80_E	2.156	1.00
22_E	63_P	2.119	1.00
30_E	66_H	2.109	1.00
5_V	34_I	2.089	1.00
101_E	105_A	2.037	1.00
35_L	55_R	1.952	1.00
23_D	26_A	1.867	1.00
102_A	106_D	1.855	1.00
24_A	88_A	1.854	1.00
37_R	69_I	1.851	1.00
50_P	53_Q	1.810	1.00
55_R	59_A	1.792	1.00
3_R	30_E	1.786	1.00
55_R	67_A	1.786	1.00
19_H	22_E	1.777	1.00
13_I	61_L	1.759	1.00
22_E	56_D	1.722	1.00
114_E	118_P	1.711	1.00
51_N	55_R	1.707	1.00
115_R	118_P	1.700	1.00
55_R	69_I	1.662	1.00
95_H	105_A	1.580	1.00
103_E	107_R	1.545	1.00
42_T	46_P	1.533	1.00
37_R	71_H	1.518	1.00
83_D	107_R	1.484	1.00
12_L	49_L	1.477	1.00
56_D	59_A	1.476	1.00
13_I	57_V	1.471	1.00
94_H	97_A	1.465	1.00
19_H	23_D	1.438	1.00
25_A	30_E	1.377	1.00
15_P	128_L	1.360	1.00
18_V	57_V	1.342	1.00
49_L	53_Q	1.334	1.00
13_I	18_V	1.319	1.00
15_P	53_Q	1.312	1.00
24_A	31_L	1.279	1.00
72_P	77_A	1.275	1.00
39_E	43_H	1.272	1.00
48_V	134_A	1.244	1.00
10_F	20_Y	1.242	1.00
39_E	71_H	1.210	1.00
91_F	114_E	1.180	1.00
15_P	57_V	1.180	1.00
104_L	109_L	1.166	1.00
132_D	135_D	1.142	1.00
76_F	103_E	1.142	1.00
4_V	88_A	1.140	1.00
87_I	100_I	1.091	1.00
75_I	87_I	1.068	0.99
99_A	103_E	1.061	0.99
13_I	58_V	1.052	0.99
27_M	88_A	1.017	0.99
2_T	110_D	1.011	0.99
22_E	26_A	1.011	0.99
36_A	40_N	0.990	0.99
35_L	58_V	0.968	0.99
2_T	86_V	0.965	0.99
27_M	86_V	0.960	0.99
110_D	114_E	0.936	0.99
34_I	78_P	0.934	0.99
113_V	116_A	0.928	0.99
34_I	68_R	0.916	0.98
130_S	134_A	0.912	0.98
114_E	117_S	0.906	0.98
37_R	51_N	0.892	0.98
21_L	24_A	0.890	0.98
80_E	106_D	0.889	0.98
80_E	103_E	0.877	0.98
100_I	104_L	0.875	0.98
25_A	62_D	0.871	0.98
99_A	102_A	0.858	0.98
99_A	104_L	0.854	0.97
32_H	82_I	0.853	0.97
33_V	58_V	0.847	0.97
79_I	87_I	0.842	0.97
15_P	19_H	0.841	0.97
28_G	88_A	0.841	0.97
128_L	132_D	0.825	0.97
132_D	136_R	0.821	0.97
42_T	45_D	0.811	0.96
80_E	107_R	0.806	0.96
49_L	133_I	0.800	0.96
18_V	60_A	0.796	0.96
60_A	63_P	0.790	0.96
36_A	70_G	0.788	0.96
129_S	132_D	0.787	0.96
6_A	20_Y	0.779	0.96
21_L	63_P	0.778	0.96
59_A	66_H	0.775	0.95
15_P	56_D	0.773	0.95
64_V	67_A	0.759	0.95
22_E	62_D	0.756	0.95
112_A	115_R	0.755	0.95
100_I	103_E	0.753	0.95
6_A	10_F	0.748	0.95
4_V	27_M	0.748	0.95
22_E	60_A	0.741	0.94
7_Q	34_I	0.739	0.94
77_A	81_A	0.727	0.94
87_I	99_A	0.724	0.94
35_L	67_A	0.723	0.93
7_Q	87_I	0.715	0.93
3_R	66_H	0.710	0.93
37_R	70_G	0.702	0.92
76_F	80_E	0.700	0.92
76_F	79_I	0.698	0.92
58_V	67_A	0.698	0.92
40_N	70_G	0.698	0.92
103_E	106_D	0.694	0.92
98_A	102_A	0.693	0.92
39_E	69_I	0.693	0.92
23_D	115_R	0.692	0.92
95_H	101_E	0.689	0.92
56_D	60_A	0.687	0.92
18_V	63_P	0.685	0.92
7_Q	70_G	0.679	0.91
42_T	47_P	0.676	0.91
39_E	42_T	0.674	0.91
33_V	82_I	0.673	0.91
15_P	18_V	0.672	0.91
66_H	69_I	0.666	0.90
5_V	87_I	0.664	0.90
105_A	110_D	0.647	0.89
33_V	64_V	0.636	0.88
99_A	107_R	0.631	0.88
90_G	93_Q	0.629	0.88
96_D	101_E	0.628	0.88
3_R	85_D	0.628	0.88
50_P	128_L	0.625	0.87
76_F	102_A	0.622	0.87
91_F	94_H	0.620	0.87
6_A	21_L	0.620	0.87
45_D	49_L	0.619	0.87
89_L	93_Q	0.616	0.87
70_G	93_Q	0.614	0.86
39_E	51_N	0.611	0.86
49_L	57_V	0.610	0.86
18_V	61_L	0.610	0.86
95_H	99_A	0.607	0.86
104_L	107_R	0.600	0.85
7_Q	89_L	0.595	0.85
40_N	43_H	0.594	0.85
98_A	113_V	0.582	0.83
22_E	59_A	0.577	0.83
38_R	51_N	0.577	0.83
80_E	83_D	0.577	0.83
3_R	84_P	0.572	0.82
110_D	115_R	0.571	0.82
99_A	105_A	0.569	0.82
102_A	105_A	0.568	0.82
93_Q	113_V	0.563	0.81
28_G	86_V	0.559	0.81
19_H	116_A	0.559	0.81
52_R	69_I	0.557	0.81
25_A	31_L	0.556	0.81
98_A	101_E	0.556	0.81
76_F	99_A	0.556	0.81
79_I	84_P	0.555	0.80
9_T	36_A	0.551	0.80
39_E	50_P	0.547	0.79
15_P	49_L	0.546	0.79
101_E	104_L	0.541	0.79
134_A	137_V	0.539	0.78
15_P	50_P	0.538	0.78
27_M	112_A	0.537	0.78
4_V	86_V	0.537	0.78
83_D	106_D	0.537	0.78
43_H	47_P	0.536	0.78
109_L	114_E	0.534	0.78
97_A	101_E	0.534	0.78
110_D	113_V	0.529	0.77
6_A	36_A	0.523	0.76
32_H	84_P	0.511	0.75
23_D	114_E	0.511	0.75
87_I	98_A	0.511	0.75
93_Q	98_A	0.510	0.75
68_R	78_P	0.507	0.74
2_T	29_D	0.507	0.74
21_L	61_L	0.502	0.73
59_A	136_R	0.501	0.73
78_P	82_I	0.500	0.73

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
3elbA	2	0.8904	100	0.365	Contact Map
4mvcA	2	0.9384	99.9	0.445	Contact Map
3hl4A	2	0.9247	99.9	0.475	Contact Map
3glvA	2	0.8219	99.9	0.531	Contact Map
2b7lA	2	0.774	99.9	0.534	Contact Map
1cozA	2	0.8493	99.9	0.547	Contact Map
3do8A	2	0.8425	99.7	0.624	Contact Map
3k9wA	5	0.9315	99.6	0.65	Contact Map
1mrzA	2	0.9452	99.6	0.656	Contact Map
3op1A	4	0.9452	99.5	0.664	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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