YYCI - BACSU - GREMLIN Contacts

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YYCI - Two-component system YycFG regulatory protein

UniProt:	Q45612	Sequences: MEWNKTKSIFIVAFLILDIFLGYQFFQKWQATGKEYEVIKNDVEHDMKADHITYEGLNKEATEGYRITANQKSFSKEEIEALKDQKPLMDMPSDDHKVTSLKMKFANPIALSKKDIEDDAQALVSSKIQDGEKYKLWKVDKSKKEIIFFQTYEGHYIYQKTDNPSNMIGQVVLHLNGKNEVVSYDQTTLETFKQIQKESLITEMDAVELLYYQNQLKEYSTVKSCKFGYVAQYPLTSTQVLAPVWRITVEYEKKVNGEKKTVQEYFTVNALESTILDTDQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	280 (251)
Sequences:	453 (389)
Seq/√Len:	24.6

BACSU - YYCI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
176_N	180_E	5.437	1.00
223_K	250_E	4.611	1.00
85_Q	103_M	4.528	1.00
148_F	173_L	3.570	1.00
105_F	108_P	3.532	1.00
3_W	7_K	3.410	1.00
3_W	11_I	2.981	1.00
124_V	171_V	2.898	1.00
7_K	11_I	2.810	0.99
134_Y	186_Q	2.789	0.99
8_S	11_I	2.515	0.99
231_A	239_Q	2.499	0.99
68_T	240_V	2.402	0.98
225_C	247_I	2.325	0.98
58_N	203_E	2.297	0.98
2_E	9_I	2.230	0.97
5_K	9_I	2.146	0.96
3_W	8_S	2.126	0.96
110_A	180_E	2.101	0.96
51_H	219_Y	2.066	0.96
124_V	148_F	2.018	0.95
203_E	225_C	2.015	0.95
6_T	10_F	1.995	0.95
54_Y	222_V	1.991	0.95
145_E	172_V	1.939	0.94
4_N	7_K	1.935	0.94
18_D	25_F	1.878	0.93
239_Q	242_A	1.876	0.93
131_G	186_Q	1.822	0.91
105_F	123_L	1.794	0.91
130_D	133_K	1.785	0.91
2_E	5_K	1.774	0.90
6_T	20_F	1.752	0.90
50_D	211_Y	1.693	0.88
120_A	205_D	1.677	0.87
268_V	275_I	1.650	0.87
55_E	222_V	1.638	0.86
137_W	149_F	1.629	0.86
176_N	179_N	1.624	0.86
5_K	48_K	1.621	0.86
131_G	184_Y	1.608	0.85
10_F	249_V	1.606	0.85
224_S	248_T	1.584	0.84
128_I	134_Y	1.582	0.84
123_L	127_K	1.570	0.84
146_I	173_L	1.559	0.83
1_M	14_F	1.557	0.83
247_I	266_F	1.555	0.83
206_A	247_I	1.554	0.83
15_L	175_L	1.538	0.82
1_M	21_L	1.528	0.82
101_L	154_G	1.528	0.82
216_L	233_Y	1.510	0.81
200_L	271_L	1.499	0.81
80_E	178_K	1.489	0.80
82_L	85_Q	1.477	0.80
207_V	247_I	1.473	0.80
3_W	228_G	1.463	0.79
14_F	21_L	1.461	0.79
269_N	272_E	1.448	0.78
3_W	267_T	1.447	0.78
69_A	189_L	1.442	0.78
57_L	225_C	1.423	0.77
6_T	203_E	1.415	0.77
157_I	192_F	1.395	0.76
69_A	241_L	1.393	0.76
86_K	128_I	1.393	0.76
241_L	267_T	1.349	0.73
178_K	207_V	1.325	0.72
103_M	128_I	1.297	0.70
156_Y	186_Q	1.293	0.70
50_D	220_S	1.286	0.69
22_G	26_F	1.285	0.69
147_I	268_V	1.269	0.68
10_F	211_Y	1.260	0.68
18_D	81_A	1.257	0.68
71_Q	222_V	1.256	0.68
54_Y	220_S	1.248	0.67
66_R	269_N	1.248	0.67
85_Q	108_P	1.235	0.66
103_M	184_Y	1.228	0.66
230_V	270_A	1.214	0.65
135_K	151_T	1.213	0.65
5_K	101_L	1.206	0.64
9_I	13_A	1.206	0.64
136_L	271_L	1.193	0.63
10_F	50_D	1.190	0.63
244_V	267_T	1.189	0.63
7_K	158_Y	1.183	0.63
56_G	109_I	1.181	0.63
48_K	113_K	1.167	0.62
19_I	138_K	1.163	0.61
150_Q	186_Q	1.154	0.61
146_I	175_L	1.150	0.61
171_V	184_Y	1.145	0.60
149_F	173_L	1.130	0.59
12_V	16_I	1.130	0.59
158_Y	269_N	1.121	0.59
101_L	106_A	1.117	0.58
14_F	184_Y	1.112	0.58
17_L	21_L	1.111	0.58
158_Y	241_L	1.099	0.57
207_V	274_T	1.097	0.57
45_H	49_A	1.093	0.57
4_N	11_I	1.088	0.56
15_L	54_Y	1.063	0.54
158_Y	228_G	1.056	0.54
133_K	188_T	1.054	0.54
208_E	222_V	1.052	0.54
2_E	220_S	1.047	0.53
2_E	123_L	1.045	0.53
126_S	218_E	1.043	0.53
47_M	276_L	1.040	0.53
41_N	88_L	1.036	0.53
201_I	273_S	1.034	0.52
18_D	123_L	1.031	0.52
59_K	196_Q	1.029	0.52
149_F	159_Q	1.026	0.52
227_F	242_A	1.020	0.51
134_Y	184_Y	1.018	0.51
157_I	240_V	1.017	0.51
7_K	17_L	1.014	0.51
2_E	58_N	1.012	0.51
140_D	187_T	1.005	0.50
64_G	267_T	1.001	0.50
40_K	189_L	0.991	0.49
9_I	17_L	0.987	0.49
10_F	64_G	0.986	0.49
207_V	222_V	0.985	0.49
11_I	231_A	0.983	0.49
19_I	189_L	0.983	0.49
184_Y	268_V	0.980	0.49
14_F	134_Y	0.973	0.48
86_K	207_V	0.965	0.47
213_Q	247_I	0.962	0.47
29_W	205_D	0.960	0.47
6_T	38_V	0.958	0.47
9_I	150_Q	0.958	0.47
136_L	139_V	0.953	0.47
130_D	188_T	0.945	0.46
37_E	237_S	0.943	0.46
185_D	202_T	0.930	0.45
12_V	107_N	0.930	0.45
2_E	181_V	0.930	0.45
206_A	268_V	0.929	0.45
75_S	222_V	0.928	0.45
109_I	226_K	0.925	0.45
7_K	24_Q	0.925	0.45
7_K	239_Q	0.923	0.44
186_Q	241_L	0.922	0.44
87_P	106_A	0.915	0.44
16_I	73_S	0.912	0.44
229_Y	270_A	0.909	0.43
9_I	181_V	0.907	0.43
232_Q	238_T	0.903	0.43
159_Q	168_I	0.899	0.43
102_K	185_D	0.898	0.43
111_L	152_Y	0.896	0.43
9_I	20_F	0.890	0.42
6_T	216_L	0.889	0.42
201_I	234_P	0.883	0.42
52_I	220_S	0.879	0.41
101_L	190_E	0.877	0.41
77_E	221_T	0.875	0.41
184_Y	217_K	0.875	0.41
99_T	222_V	0.873	0.41
27_Q	98_V	0.871	0.41
10_F	231_A	0.870	0.41
18_D	105_F	0.853	0.40
184_Y	245_W	0.851	0.39
27_Q	148_F	0.850	0.39
81_A	101_L	0.846	0.39
208_E	268_V	0.845	0.39
195_I	240_V	0.843	0.39
87_P	132_E	0.841	0.39
137_W	275_I	0.838	0.39
3_W	241_L	0.834	0.38
136_L	154_G	0.825	0.38
10_F	74_F	0.822	0.37
3_W	6_T	0.822	0.37
18_D	86_K	0.821	0.37
134_Y	210_L	0.818	0.37
23_Y	191_T	0.818	0.37
67_I	145_E	0.817	0.37
217_K	220_S	0.817	0.37
18_D	50_D	0.811	0.37
22_G	175_L	0.803	0.36
82_L	109_I	0.801	0.36
3_W	246_R	0.800	0.36
203_E	267_T	0.798	0.36
183_S	273_S	0.789	0.35
2_E	266_F	0.788	0.35
56_G	200_L	0.784	0.35
3_W	203_E	0.784	0.35
15_L	22_G	0.780	0.35
10_F	25_F	0.775	0.34
48_K	122_A	0.774	0.34
186_Q	210_L	0.770	0.34
135_K	156_Y	0.765	0.34
143_K	197_K	0.764	0.34
17_L	273_S	0.763	0.34
83_K	146_I	0.762	0.33
157_I	190_E	0.755	0.33
208_E	275_I	0.754	0.33
22_G	25_F	0.752	0.33
126_S	178_K	0.750	0.33
122_A	180_E	0.750	0.33
10_F	186_Q	0.750	0.33
148_F	202_T	0.749	0.33
150_Q	187_T	0.746	0.32
57_L	176_N	0.745	0.32
104_K	221_T	0.741	0.32
4_N	226_K	0.740	0.32
18_D	142_S	0.735	0.32
35_E	47_M	0.734	0.32
154_G	192_F	0.733	0.32
2_E	98_V	0.732	0.32
125_S	169_G	0.732	0.32
69_A	134_Y	0.728	0.31
140_D	143_K	0.727	0.31
11_I	203_E	0.722	0.31
18_D	110_A	0.721	0.31
12_V	60_E	0.719	0.31
3_W	266_F	0.718	0.31
48_K	110_A	0.714	0.30
27_Q	181_V	0.713	0.30
143_K	277_D	0.707	0.30
119_D	171_V	0.707	0.30
2_E	105_F	0.704	0.30
186_Q	216_L	0.703	0.30
64_G	227_F	0.697	0.29
5_K	271_L	0.693	0.29
128_I	171_V	0.692	0.29
12_V	175_L	0.692	0.29
173_L	181_V	0.691	0.29
59_K	126_S	0.690	0.29
89_M	105_F	0.684	0.29
128_I	184_Y	0.684	0.29
246_R	265_Y	0.683	0.29
213_Q	271_L	0.682	0.29
13_A	214_N	0.678	0.28
195_I	241_L	0.676	0.28
9_I	220_S	0.674	0.28
4_N	24_Q	0.673	0.28
47_M	152_Y	0.672	0.28
68_T	230_V	0.671	0.28
87_P	225_C	0.671	0.28
18_D	185_D	0.667	0.28
121_Q	191_T	0.664	0.28
40_K	45_H	0.661	0.27
12_V	180_E	0.661	0.27
7_K	267_T	0.658	0.27
40_K	59_K	0.658	0.27
43_V	207_V	0.656	0.27
134_Y	275_I	0.656	0.27
19_I	35_E	0.655	0.27
222_V	238_T	0.655	0.27
230_V	267_T	0.654	0.27
46_D	253_K	0.652	0.27
222_V	249_V	0.652	0.27
19_I	145_E	0.651	0.27
82_L	103_M	0.650	0.27
215_Q	277_D	0.650	0.27
3_W	44_E	0.647	0.27
7_K	238_T	0.640	0.26
3_W	58_N	0.639	0.26
15_L	24_Q	0.637	0.26
64_G	195_I	0.634	0.26
68_T	232_Q	0.632	0.26
3_W	231_A	0.628	0.26
89_M	174_H	0.626	0.25
158_Y	193_K	0.625	0.25
19_I	63_E	0.625	0.25
110_A	226_K	0.625	0.25
85_Q	89_M	0.623	0.25
7_K	212_Y	0.620	0.25
24_Q	108_P	0.620	0.25
252_E	275_I	0.619	0.25
27_Q	175_L	0.618	0.25
207_V	228_G	0.617	0.25
201_I	206_A	0.615	0.25
78_E	153_E	0.615	0.25
3_W	24_Q	0.614	0.25
112_S	119_D	0.614	0.25
54_Y	217_K	0.614	0.25
137_W	246_R	0.612	0.25
108_P	176_N	0.612	0.25
155_H	226_K	0.610	0.25
173_L	275_I	0.610	0.25
141_K	144_K	0.610	0.25
172_V	218_E	0.607	0.24
135_K	193_K	0.607	0.24
63_E	216_L	0.606	0.24
148_F	169_G	0.605	0.24
35_E	222_V	0.605	0.24
181_V	223_K	0.604	0.24
150_Q	228_G	0.602	0.24
69_A	231_A	0.593	0.24
57_L	270_A	0.591	0.24
151_T	182_V	0.589	0.23
57_L	131_G	0.587	0.23
15_L	77_E	0.587	0.23
153_E	203_E	0.584	0.23
107_N	130_D	0.583	0.23
63_E	78_E	0.583	0.23
157_I	272_E	0.582	0.23
99_T	104_K	0.581	0.23
150_Q	222_V	0.581	0.23
77_E	102_K	0.579	0.23
236_T	276_L	0.579	0.23
56_G	67_I	0.576	0.23
196_Q	248_T	0.574	0.23
134_Y	245_W	0.574	0.23
14_F	186_Q	0.573	0.23
128_I	190_E	0.573	0.23
46_D	246_R	0.572	0.23
47_M	167_M	0.569	0.22
4_N	13_A	0.569	0.22
4_N	99_T	0.567	0.22
168_I	228_G	0.566	0.22
27_Q	129_Q	0.561	0.22
12_V	15_L	0.561	0.22
1_M	229_Y	0.560	0.22
67_I	220_S	0.558	0.22
233_Y	240_V	0.556	0.22
90_D	97_K	0.555	0.22
152_Y	194_Q	0.554	0.22
5_K	138_K	0.554	0.22
103_M	240_V	0.553	0.22
50_D	195_I	0.552	0.22
145_E	151_T	0.551	0.22
68_T	239_Q	0.549	0.21
149_F	245_W	0.549	0.21
158_Y	244_V	0.548	0.21
211_Y	270_A	0.547	0.21
125_S	238_T	0.546	0.21
26_F	124_V	0.546	0.21
173_L	212_Y	0.545	0.21
69_A	234_P	0.545	0.21
75_S	138_K	0.541	0.21
109_I	138_K	0.540	0.21
4_N	17_L	0.538	0.21
80_E	104_K	0.535	0.21
75_S	266_F	0.535	0.21
135_K	275_I	0.533	0.21
241_L	244_V	0.532	0.21
136_L	196_Q	0.532	0.21
192_F	227_F	0.529	0.20
12_V	172_V	0.529	0.20
27_Q	167_M	0.529	0.20
46_D	198_E	0.528	0.20
184_Y	273_S	0.528	0.20
15_L	19_I	0.528	0.20
43_V	128_I	0.525	0.20
9_I	222_V	0.523	0.20
184_Y	210_L	0.521	0.20
5_K	250_E	0.518	0.20
148_F	198_E	0.518	0.20
148_F	201_I	0.515	0.20
85_Q	207_V	0.515	0.20
6_T	54_Y	0.515	0.20
156_Y	159_Q	0.515	0.20
4_N	148_F	0.513	0.20
151_T	154_G	0.513	0.20
16_I	217_K	0.511	0.20
136_L	185_D	0.510	0.20
30_Q	179_N	0.510	0.20
194_Q	268_V	0.508	0.20
61_A	268_V	0.507	0.19
14_F	17_L	0.506	0.19
13_A	136_L	0.505	0.19
40_K	154_G	0.505	0.19
52_I	222_V	0.503	0.19
12_V	63_E	0.502	0.19
103_M	125_S	0.501	0.19
98_V	178_K	0.500	0.19

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
2o3oA	2	0.8821	100	0.394	Contact Map
2fgtA	1	0.8607	99.8	0.703	Contact Map
4k90B	1	0.6143	99.4	0.788	Contact Map
3nqzA	1	0.5786	98.3	0.861	Contact Map
4exrA	2	0.5071	95.3	0.91	Contact Map
2gu3A	1	0.4357	92.8	0.919	Contact Map
4ipbA	1	0.45	27.2	0.954	Contact Map
4cbcA	3	0.1	25.8	0.954	Contact Map
2kgyA	1	0.3071	25.4	0.955	Contact Map
1sghB	1	0.0464	22.6	0.956	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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