YOQD - BACSU - GREMLIN Contacts

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YOQD - SPBc2 prophage-derived putative antirepressor protein YoqD

UniProt:	O34449	Sequences: MESYLTVIEQNGQLLVDSREVAEMVGKRHTDLLRSIDGYVAILLNAKLRSVEFFLESTYKDATGRSLKHFHLTRKGCDMVANKMTGAKGVLFTAQYVSKFEEMEKALKARPSLIDTYLDMNEDERAIAYFTERKAKRELQEQLTLAEPKVEKYDRFLNTDGLMKIGQVAKAIGIKGMGQNNLFRFLRENKVLIDGTNKNAPYQKYVERGFFQVKTQETSVGIKTITLVTPKGADFIVDLLKKHGHKREIAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	251 (218)
Sequences:	1474 (1202)
Seq/√Len:	81.4

BACSU - YOQD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_A	150_V	4.636	1.00
143_L	146_A	3.629	1.00
62_A	65_R	3.537	1.00
132_E	136_K	3.376	1.00
149_K	154_D	3.144	1.00
63_T	67_L	3.012	1.00
139_L	143_L	2.970	1.00
61_D	65_R	2.582	1.00
136_K	139_L	2.531	1.00
62_A	67_L	2.518	1.00
185_F	189_N	2.418	1.00
162_L	212_Q	2.417	1.00
142_Q	146_A	2.342	1.00
79_M	93_T	2.337	1.00
31_D	34_R	2.165	1.00
34_R	38_G	2.121	1.00
136_K	140_Q	2.101	1.00
35_S	80_V	2.025	1.00
129_Y	132_E	1.972	1.00
139_L	142_Q	1.892	1.00
118_L	122_E	1.809	1.00
19_R	23_E	1.797	1.00
187_R	199_N	1.733	1.00
162_L	227_L	1.713	1.00
17_D	71_H	1.693	1.00
114_I	121_N	1.677	1.00
125_R	129_Y	1.672	1.00
118_L	121_N	1.653	1.00
93_T	97_V	1.650	1.00
75_K	101_E	1.648	1.00
127_I	130_F	1.629	1.00
119_D	122_E	1.625	1.00
126_A	132_E	1.613	1.00
75_K	79_M	1.603	1.00
130_F	134_K	1.603	1.00
135_A	140_Q	1.585	1.00
59_Y	65_R	1.579	1.00
33_L	37_D	1.568	1.00
126_A	129_Y	1.564	1.00
79_M	94_A	1.558	1.00
133_R	136_K	1.539	0.99
61_D	67_L	1.470	0.99
75_K	94_A	1.467	0.99
64_G	67_L	1.465	0.99
79_M	97_V	1.429	0.99
22_A	27_K	1.426	0.99
73_T	76_G	1.426	0.99
114_I	120_M	1.424	0.99
82_N	97_V	1.415	0.99
83_K	93_T	1.392	0.99
77_C	81_A	1.388	0.99
82_N	96_Y	1.360	0.99
79_M	90_V	1.358	0.99
116_T	119_D	1.354	0.99
56_E	63_T	1.340	0.99
150_V	154_D	1.316	0.98
203_Q	206_V	1.311	0.98
210_F	235_F	1.296	0.98
175_K	181_N	1.291	0.98
90_V	94_A	1.285	0.98
79_M	82_N	1.271	0.98
201_P	211_F	1.269	0.98
191_V	235_F	1.263	0.98
65_R	69_H	1.263	0.98
165_I	183_F	1.262	0.98
21_V	77_C	1.262	0.98
59_Y	63_T	1.258	0.98
135_A	139_L	1.234	0.98
170_K	193_I	1.220	0.97
125_R	130_F	1.219	0.97
79_M	83_K	1.207	0.97
27_K	86_G	1.203	0.97
82_N	93_T	1.199	0.97
168_V	228_V	1.176	0.97
90_V	93_T	1.167	0.97
184_R	188_E	1.163	0.96
27_K	34_R	1.162	0.96
28_R	31_D	1.156	0.96
88_K	91_L	1.153	0.96
56_E	67_L	1.148	0.96
211_F	228_V	1.146	0.96
183_F	199_N	1.132	0.96
31_D	55_L	1.123	0.96
32_L	35_S	1.123	0.96
84_M	92_F	1.121	0.96
128_A	131_T	1.120	0.96
60_K	65_R	1.114	0.96
97_V	101_E	1.113	0.95
58_T	61_D	1.106	0.95
211_F	226_T	1.097	0.95
164_K	227_L	1.095	0.95
76_G	79_M	1.095	0.95
26_G	86_G	1.090	0.95
63_T	66_S	1.079	0.95
28_R	34_R	1.074	0.95
62_A	66_S	1.063	0.94
216_Q	223_K	1.059	0.94
74_R	78_D	1.056	0.94
119_D	123_D	1.054	0.94
27_K	35_S	1.051	0.94
37_D	68_K	1.050	0.94
115_D	122_E	1.042	0.94
25_V	84_M	1.038	0.93
59_Y	67_L	1.031	0.93
191_V	239_L	1.029	0.93
96_Y	104_E	1.027	0.93
76_G	93_T	1.027	0.93
192_L	199_N	1.024	0.93
124_E	128_A	1.020	0.93
168_V	233_A	1.019	0.93
57_S	61_D	1.018	0.93
202_Y	205_Y	1.009	0.92
27_K	85_T	1.009	0.92
116_T	121_N	1.009	0.92
18_S	32_L	0.990	0.92
114_I	119_D	0.987	0.92
43_L	47_K	0.985	0.92
18_S	36_I	0.977	0.91
119_D	132_E	0.972	0.91
60_K	67_L	0.961	0.91
174_I	181_N	0.954	0.90
114_I	122_E	0.950	0.90
31_D	35_S	0.948	0.90
61_D	64_G	0.947	0.90
128_A	133_R	0.946	0.90
15_L	71_H	0.943	0.90
142_Q	147_E	0.941	0.90
191_V	205_Y	0.934	0.89
123_D	130_F	0.933	0.89
56_E	65_R	0.930	0.89
78_D	101_E	0.923	0.89
74_R	104_E	0.920	0.88
167_Q	200_A	0.919	0.88
34_R	58_T	0.917	0.88
10_Q	15_L	0.913	0.88
119_D	129_Y	0.908	0.88
135_A	138_E	0.907	0.88
60_K	63_T	0.903	0.88
130_F	133_R	0.901	0.87
83_K	97_V	0.900	0.87
76_G	94_A	0.892	0.87
83_K	86_G	0.885	0.86
75_K	97_V	0.882	0.86
57_S	65_R	0.881	0.86
80_V	83_K	0.881	0.86
94_A	101_E	0.879	0.86
73_T	93_T	0.878	0.86
140_Q	143_L	0.874	0.86
144_T	147_E	0.872	0.86
132_E	135_A	0.871	0.86
110_R	114_I	0.866	0.85
119_D	125_R	0.865	0.85
86_G	96_Y	0.864	0.85
75_K	93_T	0.862	0.85
147_E	151_E	0.858	0.85
58_T	65_R	0.856	0.85
143_L	150_V	0.856	0.85
114_I	118_L	0.855	0.85
123_D	127_I	0.846	0.84
76_G	86_G	0.843	0.84
123_D	132_E	0.843	0.84
164_K	167_Q	0.841	0.84
58_T	64_G	0.837	0.83
115_D	118_L	0.836	0.83
84_M	87_A	0.835	0.83
166_G	183_F	0.832	0.83
58_T	62_A	0.829	0.83
123_D	133_R	0.828	0.83
189_N	240_L	0.826	0.82
34_R	37_D	0.824	0.82
18_S	70_F	0.823	0.82
44_L	94_A	0.815	0.82
204_K	208_R	0.815	0.82
189_N	239_L	0.813	0.81
131_T	135_A	0.813	0.81
77_C	82_N	0.808	0.81
102_E	105_K	0.806	0.81
9_E	12_G	0.805	0.81
120_M	123_D	0.801	0.80
82_N	87_A	0.801	0.80
126_A	130_F	0.787	0.79
176_G	183_F	0.785	0.79
78_D	96_Y	0.785	0.79
43_L	46_A	0.782	0.79
19_R	69_H	0.780	0.79
64_G	68_K	0.779	0.79
167_Q	213_V	0.778	0.79
193_I	197_N	0.774	0.78
127_I	134_K	0.774	0.78
94_A	97_V	0.773	0.78
72_L	78_D	0.771	0.78
103_M	107_L	0.769	0.78
85_T	90_V	0.767	0.78
112_S	118_L	0.766	0.77
22_A	35_S	0.762	0.77
76_G	97_V	0.756	0.77
80_V	86_G	0.755	0.76
44_L	47_K	0.753	0.76
214_K	227_L	0.752	0.76
18_S	47_K	0.747	0.76
35_S	84_M	0.744	0.75
17_D	20_E	0.742	0.75
112_S	122_E	0.736	0.75
127_I	132_E	0.734	0.74
122_E	125_R	0.734	0.74
79_M	86_G	0.731	0.74
166_G	176_G	0.728	0.74
134_K	138_E	0.728	0.74
56_E	62_A	0.723	0.73
114_I	117_Y	0.718	0.73
137_R	140_Q	0.715	0.72
25_V	72_L	0.713	0.72
205_Y	210_F	0.713	0.72
127_I	131_T	0.711	0.72
76_G	90_V	0.710	0.72
59_Y	62_A	0.707	0.72
192_L	201_P	0.704	0.71
114_I	125_R	0.700	0.71
86_G	93_T	0.697	0.71
201_P	213_V	0.696	0.70
33_L	57_S	0.693	0.70
123_D	126_A	0.691	0.70
84_M	89_G	0.688	0.70
59_Y	66_S	0.688	0.70
22_A	72_L	0.685	0.69
73_T	79_M	0.685	0.69
57_S	63_T	0.684	0.69
183_F	187_R	0.684	0.69
85_T	93_T	0.679	0.69
125_R	128_A	0.678	0.68
75_K	82_N	0.677	0.68
166_G	200_A	0.677	0.68
76_G	82_N	0.677	0.68
86_G	92_F	0.674	0.68
62_A	69_H	0.674	0.68
216_Q	221_G	0.673	0.68
75_K	105_K	0.671	0.68
31_D	57_S	0.671	0.68
122_E	129_Y	0.671	0.68
116_T	120_M	0.670	0.68
165_I	176_G	0.667	0.67
213_V	224_T	0.664	0.67
128_A	132_E	0.663	0.67
61_D	66_S	0.663	0.67
58_T	63_T	0.660	0.66
93_T	101_E	0.659	0.66
77_C	96_Y	0.655	0.66
132_E	139_L	0.650	0.65
35_S	86_G	0.649	0.65
149_K	153_Y	0.648	0.65
125_R	132_E	0.646	0.65
112_S	121_N	0.645	0.65
18_S	80_V	0.642	0.64
156_F	230_P	0.640	0.64
31_D	37_D	0.640	0.64
169_A	182_L	0.639	0.64
79_M	101_E	0.633	0.63
32_L	70_F	0.633	0.63
78_D	92_F	0.632	0.63
37_D	70_F	0.628	0.63
106_A	110_R	0.618	0.61
117_Y	125_R	0.617	0.61
78_D	82_N	0.613	0.61
83_K	96_Y	0.613	0.61
154_D	157_L	0.607	0.60
129_Y	136_K	0.606	0.60
83_K	87_A	0.604	0.60
25_V	80_V	0.603	0.59
131_T	134_K	0.603	0.59
117_Y	122_E	0.602	0.59
120_M	128_A	0.602	0.59
191_V	211_F	0.602	0.59
113_L	119_D	0.601	0.59
164_K	225_I	0.595	0.58
235_F	239_L	0.589	0.58
73_T	77_C	0.588	0.58
65_R	68_K	0.587	0.57
84_M	93_T	0.587	0.57
152_K	233_A	0.586	0.57
129_Y	133_R	0.585	0.57
182_L	236_I	0.583	0.57
95_Q	103_M	0.582	0.57
63_T	69_H	0.577	0.56
119_D	130_F	0.574	0.56
16_V	78_D	0.573	0.56
128_A	136_K	0.571	0.55
46_A	90_V	0.571	0.55
117_Y	120_M	0.571	0.55
171_A	233_A	0.566	0.55
56_E	59_Y	0.565	0.55
77_C	93_T	0.563	0.54
58_T	67_L	0.563	0.54
163_M	168_V	0.561	0.54
56_E	61_D	0.561	0.54
27_K	38_G	0.560	0.54
153_Y	156_F	0.559	0.54
167_Q	198_K	0.557	0.53
121_N	130_F	0.553	0.53
76_G	92_F	0.553	0.53
47_K	94_A	0.549	0.52
15_L	73_T	0.549	0.52
118_L	130_F	0.543	0.52
213_V	226_T	0.543	0.52
200_A	213_V	0.543	0.52
215_T	222_I	0.542	0.52
193_I	200_A	0.542	0.52
44_L	90_V	0.539	0.51
121_N	125_R	0.538	0.51
44_L	93_T	0.537	0.51
234_D	237_V	0.529	0.50
57_S	60_K	0.528	0.50
120_M	124_E	0.528	0.50
123_D	129_Y	0.524	0.49
139_L	146_A	0.523	0.49
170_K	203_Q	0.522	0.49
80_V	84_M	0.520	0.49
124_E	130_F	0.519	0.49
90_V	97_V	0.518	0.48
87_A	91_L	0.518	0.48
27_K	72_L	0.516	0.48
183_F	192_L	0.515	0.48
193_I	199_N	0.515	0.48
33_L	61_D	0.514	0.48
102_E	106_A	0.513	0.48
165_I	226_T	0.505	0.47
33_L	68_K	0.501	0.46
191_V	236_I	0.500	0.46

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
1p4xA	1	0.8167	95.6	0.902	Contact Map
2qlzA	2	0.7331	95.2	0.905	Contact Map
4asnA	2	0.3386	86.1	0.926	Contact Map
3hrsA	2	0.3068	84.9	0.927	Contact Map
2frhA	2	0.4741	84	0.928	Contact Map
2qwwA	2	0.4781	81.5	0.93	Contact Map
1on2A	2	0.3227	81.5	0.93	Contact Map
2qq9A	2	0.3108	80.6	0.93	Contact Map
1r7jA	2	0.3187	80.5	0.93	Contact Map
2fbhA	2	0.4382	80.3	0.93	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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