RISA - BACSU - GREMLIN Contacts

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RISA - Riboflavin synthase

UniProt:	P16440	Sequences: MFTGIIEETGTIESMKKAGHAMALTIKCSKILEDVHLGDSIAVNGICLTVTDFTKNQFTVDVMPETVKATSLNDLTKGSKVNLERAMAANGRFGGHFVSGHVDGTAEITRIEEKSNAVYYDLKMDPSLTKTLVLKGSITVDGVSLTIFGLTEDTVTISLIPHTISETIFSEKTIGSKVNIECDMIGKYMYRFLHKANENKTQQTITKAFLSENGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	215 (195)
Sequences:	3744 (2544)
Seq/√Len:	182.2

ECOLI - RISA
BACSU - RISA
HALSA - Q9HMB2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_A	91_G	3.072	1.00
106_A	122_L	2.551	1.00
69_A	134_L	2.483	1.00
121_D	154_T	2.370	1.00
107_E	123_K	2.330	1.00
104_G	128_L	2.321	1.00
141_D	172_K	2.290	1.00
80_K	171_E	2.237	1.00
54_T	57_Q	2.194	1.00
132_L	147_I	2.157	1.00
130_K	190_Y	2.088	1.00
52_D	59_T	2.076	1.00
109_T	123_K	2.064	1.00
11_T	27_K	2.061	1.00
13_E	27_K	2.050	1.00
87_M	93_F	2.041	1.00
131_T	190_Y	2.017	1.00
74_D	177_K	1.992	1.00
121_D	156_T	1.967	1.00
118_V	164_I	1.961	1.00
151_T	154_T	1.922	1.00
11_T	80_K	1.866	1.00
27_K	56_N	1.850	1.00
123_K	153_D	1.847	1.00
25_T	59_T	1.818	1.00
172_K	176_S	1.764	1.00
89_A	97_F	1.759	1.00
143_V	169_F	1.752	1.00
64_P	68_K	1.746	1.00
140_V	178_V	1.728	1.00
162_H	166_E	1.721	1.00
149_G	156_T	1.676	1.00
10_G	83_L	1.647	1.00
111_I	120_Y	1.627	1.00
43_V	81_V	1.608	1.00
36_H	39_D	1.588	1.00
107_E	177_K	1.585	1.00
114_K	119_Y	1.581	1.00
35_V	41_I	1.566	1.00
17_K	22_M	1.560	1.00
124_M	180_I	1.558	1.00
63_M	158_S	1.554	1.00
89_A	93_F	1.551	1.00
140_V	180_I	1.543	1.00
111_I	118_V	1.515	1.00
108_I	120_Y	1.508	1.00
108_I	172_K	1.495	1.00
75_L	79_S	1.493	1.00
8_E	28_C	1.480	1.00
46_I	70_T	1.464	1.00
123_K	154_T	1.447	1.00
25_T	57_Q	1.440	1.00
110_R	121_D	1.433	1.00
7_E	85_R	1.400	1.00
8_E	29_S	1.382	1.00
37_L	162_H	1.380	1.00
185_I	189_M	1.369	1.00
108_I	122_L	1.349	1.00
117_A	158_S	1.343	1.00
98_V	139_T	1.332	1.00
133_V	186_G	1.332	1.00
7_E	92_R	1.298	1.00
143_V	168_I	1.293	1.00
43_V	58_F	1.286	1.00
132_L	155_V	1.259	1.00
65_E	135_K	1.258	1.00
120_Y	164_I	1.254	1.00
97_F	184_M	1.253	1.00
119_Y	156_T	1.244	1.00
9_T	80_K	1.222	1.00
93_F	97_F	1.217	1.00
76_T	79_S	1.216	1.00
141_D	168_I	1.213	1.00
148_F	156_T	1.209	1.00
44_N	141_D	1.205	1.00
164_I	170_S	1.196	1.00
132_L	138_I	1.191	1.00
106_A	140_V	1.182	1.00
44_N	71_S	1.180	1.00
120_Y	159_L	1.176	1.00
122_L	157_I	1.167	1.00
148_F	158_S	1.161	1.00
133_V	191_R	1.159	1.00
124_M	132_L	1.141	1.00
97_F	185_I	1.140	1.00
133_V	184_M	1.135	1.00
65_E	69_A	1.115	1.00
51_T	61_D	1.112	1.00
71_S	177_K	1.111	1.00
68_K	114_K	1.108	1.00
27_K	57_Q	1.107	1.00
24_L	62_V	1.106	1.00
143_V	159_L	1.097	1.00
140_V	157_I	1.095	1.00
44_N	75_L	1.064	1.00
169_F	172_K	1.062	1.00
23_A	51_T	1.061	1.00
133_V	187_K	1.060	1.00
109_T	154_T	1.058	1.00
131_T	182_C	1.057	1.00
64_P	114_K	1.052	1.00
85_R	92_R	1.051	1.00
143_V	172_K	1.050	1.00
13_E	57_Q	1.049	1.00
105_T	177_K	1.046	1.00
32_L	35_V	1.033	1.00
35_V	50_V	1.027	1.00
122_L	178_V	1.027	1.00
35_V	53_F	1.026	1.00
190_Y	194_H	1.021	0.99
113_E	118_V	1.003	0.99
21_A	116_N	1.001	0.99
15_M	22_M	0.996	0.99
119_Y	158_S	0.993	0.99
30_K	33_E	0.971	0.99
80_K	170_S	0.961	0.99
111_I	173_T	0.959	0.99
99_S	184_M	0.956	0.99
10_G	26_I	0.956	0.99
108_I	178_V	0.951	0.99
50_V	53_F	0.950	0.99
134_L	149_G	0.949	0.99
106_A	180_I	0.945	0.99
14_S	25_T	0.932	0.99
88_A	93_F	0.928	0.99
9_T	168_I	0.926	0.99
63_M	148_F	0.925	0.99
34_D	85_R	0.921	0.99
173_T	176_S	0.920	0.99
138_I	155_V	0.918	0.99
124_M	129_T	0.913	0.99
39_D	94_G	0.912	0.99
34_D	92_R	0.909	0.99
86_A	92_R	0.905	0.99
108_I	111_I	0.897	0.99
71_S	179_N	0.894	0.99
12_I	81_V	0.894	0.99
120_Y	169_F	0.890	0.99
110_R	174_I	0.890	0.99
16_K	23_A	0.886	0.99
119_Y	148_F	0.885	0.99
159_L	164_I	0.878	0.98
14_S	77_K	0.875	0.98
104_G	125_D	0.874	0.98
99_S	102_V	0.871	0.98
168_I	172_K	0.863	0.98
23_A	59_T	0.851	0.98
22_M	67_V	0.845	0.98
37_L	53_F	0.842	0.98
8_E	30_K	0.841	0.98
12_I	26_I	0.834	0.98
31_I	34_D	0.833	0.98
21_A	115_S	0.831	0.98
34_D	94_G	0.831	0.98
12_I	75_L	0.827	0.98
140_V	155_V	0.815	0.98
124_M	155_V	0.809	0.97
18_A	23_A	0.809	0.97
46_I	102_V	0.804	0.97
72_L	75_L	0.799	0.97
128_L	182_C	0.798	0.97
87_M	91_G	0.796	0.97
12_I	15_M	0.790	0.97
124_M	128_L	0.788	0.97
8_E	31_I	0.787	0.97
9_T	166_E	0.785	0.97
111_I	174_I	0.776	0.97
61_D	161_P	0.776	0.97
104_G	124_M	0.773	0.97
143_V	167_T	0.772	0.97
129_T	191_R	0.769	0.96
39_D	92_R	0.768	0.96
191_R	195_K	0.757	0.96
28_C	32_L	0.751	0.96
63_M	117_A	0.750	0.96
117_A	164_I	0.737	0.96
48_L	66_T	0.735	0.95
28_C	31_I	0.734	0.95
23_A	61_D	0.722	0.95
186_G	192_F	0.721	0.95
73_N	177_K	0.718	0.95
126_P	152_E	0.712	0.95
23_A	52_D	0.709	0.94
150_L	191_R	0.705	0.94
26_I	83_L	0.701	0.94
129_T	153_D	0.696	0.94
112_E	121_D	0.694	0.94
172_K	178_V	0.694	0.94
185_I	193_L	0.694	0.94
155_V	180_I	0.689	0.94
35_V	85_R	0.689	0.94
37_L	51_T	0.688	0.94
5_I	94_G	0.688	0.94
67_V	73_N	0.686	0.93
44_N	168_I	0.683	0.93
26_I	60_V	0.682	0.93
22_M	64_P	0.681	0.93
112_E	119_Y	0.674	0.93
138_I	180_I	0.672	0.93
102_V	139_T	0.667	0.93
130_K	192_F	0.666	0.92
53_F	57_Q	0.666	0.92
43_V	83_L	0.665	0.92
189_M	193_L	0.662	0.92
25_T	54_T	0.658	0.92
31_I	35_V	0.656	0.92
49_T	162_H	0.656	0.92
20_H	64_P	0.654	0.92
186_G	189_M	0.652	0.92
62_V	66_T	0.652	0.92
7_E	91_G	0.647	0.91
3_T	93_F	0.646	0.91
112_E	156_T	0.645	0.91
88_A	92_R	0.644	0.91
13_E	25_T	0.643	0.91
133_V	188_Y	0.643	0.91
44_N	79_S	0.642	0.91
15_M	77_K	0.639	0.91
131_T	191_R	0.636	0.91
182_C	187_K	0.635	0.91
13_E	56_N	0.629	0.90
43_V	75_L	0.621	0.90
106_A	124_M	0.618	0.89
39_D	86_A	0.618	0.89
26_I	43_V	0.614	0.89
32_L	58_F	0.612	0.89
13_E	77_K	0.611	0.89
121_D	151_T	0.609	0.89
48_L	62_V	0.609	0.89
1_M	4_G	0.603	0.88
71_S	141_D	0.603	0.88
111_I	164_I	0.603	0.88
63_M	157_I	0.600	0.88
9_T	170_S	0.598	0.88
36_H	53_F	0.595	0.88
72_L	79_S	0.593	0.87
29_S	32_L	0.592	0.87
109_T	174_I	0.592	0.87
39_D	85_R	0.591	0.87
132_L	180_I	0.590	0.87
137_S	185_I	0.589	0.87
101_H	137_S	0.589	0.87
35_V	39_D	0.587	0.87
72_L	81_V	0.584	0.87
137_S	143_V	0.584	0.87
126_P	153_D	0.580	0.86
18_A	21_A	0.579	0.86
37_L	50_V	0.578	0.86
122_L	140_V	0.578	0.86
37_L	166_E	0.575	0.86
69_A	148_F	0.569	0.85
114_K	117_A	0.568	0.85
119_Y	149_G	0.568	0.85
122_L	155_V	0.568	0.85
5_I	31_I	0.566	0.85
132_L	182_C	0.562	0.84
159_L	169_F	0.561	0.84
64_P	158_S	0.560	0.84
86_A	99_S	0.558	0.84
43_V	48_L	0.557	0.84
97_F	137_S	0.554	0.84
188_Y	192_F	0.554	0.84
159_L	163_T	0.550	0.83
191_R	194_H	0.549	0.83
5_I	86_A	0.547	0.83
41_I	53_F	0.542	0.82
137_S	167_T	0.540	0.82
87_M	139_T	0.537	0.82
108_I	174_I	0.535	0.81
111_I	170_S	0.535	0.81
140_V	169_F	0.530	0.81
57_Q	60_V	0.528	0.81
143_V	170_S	0.528	0.81
104_G	182_C	0.523	0.80
67_V	72_L	0.520	0.80
82_N	168_I	0.520	0.80
109_T	121_D	0.519	0.79
63_M	116_N	0.519	0.79
182_C	186_G	0.514	0.79
98_V	103_D	0.513	0.79
96_H	144_S	0.513	0.79
137_S	161_P	0.510	0.78
69_A	135_K	0.510	0.78
65_E	68_K	0.506	0.78
39_D	53_F	0.504	0.77
43_V	60_V	0.503	0.77
129_T	150_L	0.503	0.77
37_L	52_D	0.503	0.77
113_E	174_I	0.501	0.77
21_A	63_M	0.500	0.77
28_C	58_F	0.500	0.77
130_K	195_K	0.500	0.77

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
1kzlA	1	0.9302	100	0.111	Contact Map
4g6iA	3	0.9116	100	0.122	Contact Map
1i8dA	3	0.9302	100	0.126	Contact Map
3a35A	1	0.8512	100	0.171	Contact Map
3ddyA	1	0.8093	100	0.182	Contact Map
4tkoB	1	0.5814	47	0.955	Contact Map
2wg5A	3	0.2558	28.3	0.96	Contact Map
4nbqA	3	0.4326	25.5	0.961	Contact Map
3h43A	5	0.2698	22.5	0.962	Contact Map
2f1mA	2	0.6093	20.2	0.963	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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