RISA - ECOLI - GREMLIN Contacts

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RISA - Riboflavin synthase

UniProt:	P0AFU8	Sequences: MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAMNQPGTEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11406
Length:	213 (196)
Sequences:	3742 (2517)
Seq/√Len:	179.8

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
89_K	92_D	3.106	1.00
107_A	123_F	2.602	1.00
70_I	136_Y	2.519	1.00
122_W	156_R	2.393	1.00
143_D	174_K	2.319	1.00
108_E	124_K	2.316	1.00
105_T	130_L	2.313	1.00
55_N	58_H	2.307	1.00
81_W	173_K	2.254	1.00
134_I	149_V	2.168	1.00
132_K	192_V	2.091	1.00
53_E	60_S	2.077	1.00
11_K	27_E	2.070	1.00
88_A	94_I	2.063	1.00
110_A	124_K	2.061	1.00
13_V	27_E	2.056	1.00
133_Y	192_V	2.030	1.00
75_D	179_R	1.992	1.00
122_W	158_C	1.982	1.00
119_R	166_L	1.966	1.00
153_T	156_R	1.916	1.00
27_E	57_N	1.895	1.00
11_K	81_W	1.893	1.00
124_K	155_T	1.870	1.00
25_V	60_S	1.805	1.00
90_F	98_L	1.796	1.00
174_K	178_A	1.781	1.00
142_I	180_V	1.776	1.00
145_I	171_L	1.756	1.00
65_K	69_R	1.730	1.00
164_E	168_R	1.729	1.00
151_E	158_C	1.704	1.00
10_A	84_V	1.653	1.00
112_I	121_I	1.645	1.00
36_L	42_V	1.628	1.00
8_G	28_L	1.620	1.00
37_E	40_A	1.601	1.00
44_H	82_V	1.598	1.00
115_S	120_Q	1.595	1.00
108_E	179_R	1.582	1.00
142_I	182_I	1.572	1.00
125_V	182_I	1.563	1.00
90_F	94_I	1.557	1.00
64_M	160_H	1.549	1.00
109_V	121_I	1.530	1.00
112_I	119_R	1.528	1.00
17_E	22_R	1.517	1.00
109_V	174_K	1.511	1.00
76_L	80_D	1.500	1.00
47_C	71_T	1.477	1.00
124_K	156_R	1.476	1.00
25_V	58_H	1.474	1.00
111_K	122_W	1.451	1.00
7_Q	86_R	1.398	1.00
109_V	123_F	1.383	1.00
187_Q	191_V	1.381	1.00
38_T	164_E	1.370	1.00
99_M	141_G	1.354	1.00
135_L	188_T	1.338	1.00
118_N	160_H	1.317	1.00
7_Q	93_E	1.314	1.00
44_H	59_V	1.313	1.00
145_I	170_T	1.276	1.00
98_L	186_P	1.265	1.00
134_I	157_F	1.259	1.00
121_I	166_L	1.256	1.00
120_Q	158_C	1.246	1.00
66_E	137_K	1.242	1.00
9_T	81_W	1.241	1.00
94_I	98_L	1.239	1.00
150_G	158_C	1.232	1.00
45_N	143_D	1.225	1.00
143_D	170_T	1.221	1.00
134_I	140_I	1.208	1.00
121_I	161_L	1.205	1.00
77_K	80_D	1.205	1.00
107_A	142_I	1.190	1.00
166_L	172_G	1.188	1.00
45_N	72_N	1.187	1.00
27_E	58_H	1.185	1.00
123_F	159_V	1.167	1.00
150_G	160_H	1.163	1.00
135_L	193_D	1.150	1.00
98_L	187_Q	1.141	1.00
135_L	186_P	1.141	1.00
13_V	58_H	1.136	1.00
72_N	179_R	1.134	1.00
66_E	70_I	1.131	1.00
125_V	134_I	1.130	1.00
8_G	31_H	1.127	1.00
142_I	159_V	1.119	1.00
69_R	115_S	1.116	1.00
52_T	62_D	1.106	1.00
145_I	161_L	1.098	1.00
36_L	54_I	1.085	1.00
24_H	63_L	1.083	1.00
45_N	76_L	1.082	1.00
110_A	156_R	1.081	1.00
171_L	174_K	1.076	1.00
106_T	179_R	1.073	1.00
145_I	174_K	1.069	1.00
36_L	51_V	1.064	1.00
86_R	93_E	1.060	1.00
135_L	189_Q	1.059	1.00
65_K	115_S	1.055	1.00
133_Y	184_I	1.054	1.00
23_T	52_T	1.042	1.00
126_Q	129_Q	1.042	1.00
15_I	22_R	1.020	0.99
192_V	196_E	1.013	0.99
114_T	119_R	1.006	0.99
120_Q	160_H	0.995	0.99
123_F	180_V	0.993	0.99
33_L	36_L	0.987	0.99
112_I	175_K	0.972	0.99
51_V	54_I	0.971	0.99
81_W	172_G	0.969	0.99
107_A	182_I	0.962	0.99
100_S	186_P	0.951	0.99
136_Y	151_E	0.948	0.99
10_A	26_V	0.939	0.99
89_K	94_I	0.936	0.99
109_V	180_V	0.933	0.99
35_G	93_E	0.928	0.99
140_I	157_F	0.924	0.99
31_H	34_D	0.923	0.99
9_T	170_T	0.921	0.99
64_M	150_G	0.917	0.99
21_F	117_N	0.915	0.99
175_K	178_A	0.913	0.99
35_G	86_R	0.912	0.99
125_V	131_M	0.905	0.99
40_A	95_G	0.904	0.99
72_N	181_N	0.903	0.99
120_Q	150_G	0.900	0.99
121_I	171_L	0.895	0.99
12_L	82_V	0.889	0.99
87_A	93_E	0.889	0.99
109_V	112_I	0.887	0.99
16_D	23_T	0.878	0.98
100_S	103_I	0.877	0.98
14_S	25_V	0.877	0.98
170_T	174_K	0.874	0.98
14_S	78_V	0.865	0.98
23_T	60_S	0.859	0.98
161_L	166_L	0.858	0.98
111_K	176_L	0.855	0.98
8_G	32_M	0.842	0.98
12_L	15_I	0.837	0.98
21_F	116_E	0.837	0.98
12_L	26_V	0.836	0.98
142_I	157_F	0.835	0.98
38_T	54_I	0.831	0.98
125_V	130_L	0.827	0.98
35_G	95_G	0.824	0.98
22_R	68_L	0.818	0.97
130_L	184_I	0.818	0.97
88_A	92_D	0.815	0.97
47_C	103_I	0.806	0.97
12_L	76_L	0.806	0.97
73_L	76_L	0.801	0.97
125_V	157_F	0.797	0.97
9_T	168_R	0.794	0.97
62_D	163_P	0.787	0.97
131_M	193_D	0.785	0.97
105_T	125_V	0.783	0.97
193_D	197_R	0.780	0.97
40_A	93_E	0.762	0.96
18_K	23_T	0.758	0.96
112_I	176_L	0.756	0.96
32_M	35_G	0.744	0.96
118_N	166_L	0.743	0.96
145_I	169_T	0.741	0.95
64_M	118_N	0.736	0.95
105_T	126_Q	0.734	0.95
49_L	67_T	0.730	0.95
188_T	194_T	0.724	0.95
157_F	182_I	0.724	0.95
23_T	53_E	0.719	0.95
140_I	182_I	0.719	0.95
26_V	84_V	0.714	0.94
187_Q	195_V	0.714	0.94
25_V	55_N	0.711	0.94
131_M	155_T	0.710	0.94
74_G	179_R	0.705	0.94
44_H	84_V	0.704	0.94
23_T	62_D	0.700	0.94
152_V	193_D	0.695	0.94
28_L	32_M	0.688	0.93
68_L	74_G	0.688	0.93
174_K	180_V	0.687	0.93
54_I	58_H	0.684	0.93
132_K	194_T	0.684	0.93
36_L	86_R	0.684	0.93
38_T	52_T	0.683	0.93
103_I	141_G	0.680	0.93
28_L	33_L	0.678	0.93
5_I	95_G	0.678	0.93
26_V	61_F	0.677	0.93
113_L	120_Q	0.674	0.93
188_T	191_V	0.673	0.93
32_M	36_L	0.673	0.93
128_S	154_P	0.672	0.93
113_L	122_W	0.671	0.92
45_N	170_T	0.667	0.92
7_Q	92_D	0.660	0.92
30_D	33_L	0.653	0.91
184_I	189_Q	0.651	0.91
50_T	164_E	0.649	0.91
191_V	195_V	0.649	0.91
63_L	67_T	0.644	0.91
20_N	65_K	0.643	0.91
135_L	190_A	0.637	0.90
89_K	93_E	0.635	0.90
15_I	78_V	0.633	0.90
122_W	153_T	0.629	0.90
107_A	125_V	0.626	0.90
133_Y	193_D	0.625	0.90
22_R	65_K	0.623	0.89
49_L	63_L	0.622	0.89
3_T	94_I	0.618	0.89
13_V	78_V	0.616	0.89
13_V	25_V	0.615	0.89
128_S	155_T	0.614	0.89
44_H	76_L	0.613	0.89
110_A	176_L	0.612	0.89
40_A	87_A	0.612	0.89
112_I	166_L	0.610	0.88
45_N	80_D	0.608	0.88
64_M	159_V	0.607	0.88
37_E	54_I	0.607	0.88
9_T	172_G	0.607	0.88
113_L	158_C	0.605	0.88
36_L	40_A	0.604	0.88
18_K	21_F	0.601	0.88
72_N	143_D	0.600	0.88
1_M	4_G	0.597	0.87
73_L	82_V	0.591	0.87
123_F	142_I	0.588	0.87
102_H	139_F	0.585	0.86
13_V	57_N	0.584	0.86
38_T	51_V	0.581	0.86
73_L	80_D	0.580	0.86
115_S	118_N	0.578	0.86
26_V	44_H	0.578	0.86
38_T	168_R	0.577	0.86
33_L	59_V	0.576	0.85
40_A	86_R	0.575	0.85
195_V	198_V	0.572	0.85
139_F	145_I	0.572	0.85
193_D	196_E	0.570	0.85
5_I	87_A	0.566	0.84
68_L	73_L	0.564	0.84
70_I	150_G	0.563	0.84
190_A	194_T	0.563	0.84
42_V	54_I	0.561	0.84
65_K	160_H	0.560	0.84
134_I	182_I	0.559	0.84
123_F	157_F	0.558	0.84
161_L	171_L	0.557	0.84
139_F	187_Q	0.556	0.83
120_Q	151_E	0.556	0.83
161_L	165_T	0.555	0.83
134_I	184_I	0.554	0.83
139_F	169_T	0.545	0.82
112_I	172_G	0.545	0.82
44_H	49_L	0.543	0.82
87_A	100_S	0.539	0.81
98_L	139_F	0.538	0.81
32_M	86_R	0.538	0.81
184_I	188_T	0.535	0.81
5_I	32_M	0.534	0.81
110_A	122_W	0.534	0.81
88_A	141_G	0.532	0.81
30_D	57_N	0.531	0.81
109_V	176_L	0.527	0.80
105_T	184_I	0.520	0.79
132_K	197_R	0.520	0.79
145_I	172_G	0.518	0.79
58_H	61_F	0.517	0.79
97_H	146_S	0.515	0.79
139_F	163_P	0.512	0.78
99_M	104_M	0.509	0.78
83_N	170_T	0.509	0.78
44_H	61_F	0.509	0.78
66_E	69_R	0.507	0.77
38_T	53_E	0.507	0.77
131_M	152_V	0.506	0.77
53_E	58_H	0.505	0.77
12_L	73_L	0.505	0.77
70_I	137_K	0.500	0.76
111_K	156_R	0.500	0.76
64_M	117_N	0.500	0.76
81_W	111_K	0.500	0.76

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
1i8dA	3	0.9484	100	0.076	Contact Map
1kzlA	1	0.9437	100	0.086	Contact Map
4g6iA	3	0.9202	100	0.091	Contact Map
3a35A	1	0.8638	100	0.138	Contact Map
3ddyA	1	0.8216	100	0.151	Contact Map
4tkoB	1	0.5915	45.3	0.954	Contact Map
2wg5A	3	0.2629	26.5	0.96	Contact Map
3h43A	5	0.277	19.8	0.962	Contact Map
2qcpX	1	0.3662	17	0.963	Contact Map
4nbqA	3	0.4413	15.9	0.964	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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