MED - BACSU - GREMLIN Contacts

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MED - Transcriptional activator protein med

UniProt:	O32436	Sequences: MITRLVMIFSVLLLLSGCGQTPFKGKIEKVGMLFPDTINDLVWGTKGYKGLLNIQSKYNVDVYYKEGVKTEEDIINAIEDFHKRGVNLLYGHGSEYAEVFNLVGEDYPDMEFVISNAKAKADNVTSVHFSGEAMGFFGGMTAAHMSKTNQVGVIASFTWQPEVDGFIKGAKYENPDIEVNTKYTDHWDDDTTAVKLYQKMKNEGADVVYPAGDGYNVPVIQQIKKDGLYAIGYVTDQSDLGENTVLTSTVQNVDKAYEIIAEQFNKGTLEGGDHYYDLNTGVVEMGTFSPLVDQDFQQRIAKLIKTYNKTGELPKNE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	317 (306)
Sequences:	3747 (2794)
Seq/√Len:	159.7

BACSU - MED YUFN
HALSA - Q9HR20 Q9HRA0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
306_T	312_E	4.692	1.00
136_F	172_Y	3.738	1.00
294_Q	298_Q	3.517	1.00
91_G	100_F	3.479	1.00
305_K	310_T	3.468	1.00
170_A	177_I	3.436	1.00
262_E	266_K	3.274	1.00
302_K	306_T	3.051	1.00
149_N	174_N	3.043	1.00
201_K	228_L	2.968	1.00
75_I	102_L	2.703	1.00
140_M	303_L	2.665	1.00
79_E	106_D	2.579	1.00
304_I	308_N	2.570	1.00
45_T	49_K	2.568	1.00
151_V	170_A	2.548	1.00
150_Q	178_E	2.536	1.00
146_S	149_N	2.516	1.00
144_H	299_R	2.509	1.00
57_K	258_E	2.471	1.00
184_T	215_Y	2.410	1.00
150_Q	180_N	2.408	1.00
39_N	45_T	2.357	1.00
53_N	258_E	2.195	1.00
299_R	302_K	2.175	1.00
146_S	206_D	2.145	1.00
277_D	280_T	2.140	1.00
145_M	293_D	2.063	1.00
82_H	112_F	2.060	1.00
293_D	296_F	2.052	1.00
52_L	55_Q	2.018	1.00
301_A	304_I	1.966	1.00
138_G	285_M	1.939	1.00
301_A	305_K	1.936	1.00
140_M	173_E	1.921	1.00
297_Q	301_A	1.920	1.00
82_H	107_Y	1.901	1.00
150_Q	205_A	1.899	1.00
154_I	219_V	1.870	1.00
134_M	249_T	1.854	1.00
259_I	263_Q	1.853	1.00
79_E	107_Y	1.849	1.00
141_T	300_I	1.814	1.00
53_N	57_K	1.765	1.00
298_Q	302_K	1.743	1.00
129_F	256_A	1.738	1.00
48_Y	52_L	1.733	1.00
52_L	56_S	1.709	1.00
140_M	172_Y	1.699	1.00
167_I	171_K	1.696	1.00
186_H	189_D	1.692	1.00
172_Y	303_L	1.678	1.00
202_N	226_D	1.658	1.00
284_E	304_I	1.657	1.00
138_G	231_I	1.653	1.00
193_A	215_Y	1.637	1.00
305_K	308_N	1.635	1.00
130_S	277_D	1.625	1.00
89_L	110_M	1.624	1.00
131_G	161_P	1.622	1.00
31_G	81_F	1.589	1.00
38_I	64_Y	1.576	1.00
306_T	313_L	1.573	1.00
145_M	296_F	1.513	1.00
294_Q	297_Q	1.512	1.00
54_I	261_A	1.509	1.00
65_K	81_F	1.498	1.00
194_V	225_K	1.474	1.00
263_Q	268_T	1.459	1.00
278_L	308_N	1.438	1.00
163_V	167_I	1.435	1.00
197_Y	208_V	1.426	1.00
63_Y	86_V	1.426	1.00
194_V	198_Q	1.424	1.00
190_D	215_Y	1.413	1.00
232_G	237_Q	1.396	1.00
143_A	146_S	1.377	1.00
180_N	205_A	1.372	1.00
78_I	91_G	1.369	1.00
281_G	284_E	1.363	1.00
54_I	58_Y	1.361	1.00
14_L	17_G	1.347	1.00
58_Y	258_E	1.346	1.00
31_G	86_V	1.333	1.00
28_E	264_F	1.331	1.00
143_A	177_I	1.329	1.00
299_R	303_L	1.328	1.00
201_K	223_I	1.312	1.00
58_Y	262_E	1.310	1.00
130_S	133_A	1.283	1.00
11_V	14_L	1.281	1.00
306_T	310_T	1.280	1.00
133_A	279_N	1.258	1.00
198_Q	202_N	1.252	1.00
298_Q	301_A	1.247	1.00
79_E	83_K	1.239	1.00
29_K	61_D	1.233	1.00
194_V	221_Q	1.227	1.00
252_N	255_K	1.217	1.00
105_E	121_A	1.215	1.00
29_K	86_V	1.211	1.00
47_G	257_Y	1.204	1.00
137_F	300_I	1.203	1.00
148_T	206_D	1.202	1.00
53_N	254_D	1.198	1.00
27_I	61_D	1.176	1.00
138_G	249_T	1.169	1.00
57_K	262_E	1.165	1.00
150_Q	204_G	1.158	1.00
83_K	107_Y	1.156	1.00
137_F	304_I	1.149	1.00
303_L	306_T	1.145	1.00
73_D	76_N	1.142	1.00
141_T	247_T	1.141	1.00
136_F	303_L	1.136	1.00
152_G	205_A	1.128	1.00
184_T	196_L	1.124	1.00
220_I	245_V	1.122	1.00
18_C	21_T	1.116	1.00
88_L	261_A	1.115	1.00
289_S	297_Q	1.096	1.00
144_H	296_F	1.090	0.99
146_S	207_V	1.089	0.99
49_K	52_L	1.088	0.99
180_N	203_E	1.086	0.99
258_E	262_E	1.086	0.99
134_M	283_V	1.085	0.99
34_F	64_Y	1.079	0.99
101_N	105_E	1.077	0.99
55_Q	61_D	1.074	0.99
79_E	103_V	1.073	0.99
36_D	44_G	1.053	0.99
146_S	170_A	1.050	0.99
97_A	117_A	1.046	0.99
125_T	269_L	1.045	0.99
75_I	79_E	1.042	0.99
78_I	103_V	1.042	0.99
222_Q	225_K	1.036	0.99
75_I	103_V	1.032	0.99
28_E	265_N	1.028	0.99
224_K	243_N	1.025	0.99
247_T	286_G	1.023	0.99
195_K	198_Q	1.019	0.99
30_V	88_L	1.019	0.99
51_L	62_V	1.011	0.99
15_L	18_C	1.009	0.99
7_M	10_S	1.005	0.99
252_N	284_E	1.001	0.99
182_K	200_M	1.000	0.99
259_I	262_E	0.997	0.99
152_G	200_M	0.996	0.99
111_E	269_L	0.993	0.99
198_Q	222_Q	0.990	0.99
143_A	173_E	0.990	0.99
227_G	244_T	0.990	0.99
10_S	13_L	0.981	0.99
229_Y	246_L	0.981	0.99
9_F	12_L	0.980	0.99
79_E	82_H	0.979	0.99
81_F	86_V	0.978	0.99
92_H	115_S	0.976	0.99
48_Y	64_Y	0.974	0.99
38_I	48_Y	0.967	0.99
207_V	231_I	0.964	0.99
219_V	230_A	0.964	0.99
201_K	208_V	0.961	0.99
184_T	193_A	0.960	0.99
230_A	244_T	0.953	0.99
18_C	24_K	0.945	0.99
50_G	254_D	0.939	0.98
121_A	124_V	0.932	0.98
220_I	230_A	0.931	0.98
192_T	195_K	0.926	0.98
67_G	77_A	0.915	0.98
174_N	177_I	0.915	0.98
78_I	100_F	0.914	0.98
85_G	110_M	0.912	0.98
140_M	299_R	0.911	0.98
55_Q	62_V	0.910	0.98
104_G	121_A	0.904	0.98
250_V	284_E	0.904	0.98
101_N	124_V	0.902	0.98
130_S	275_Y	0.900	0.98
255_K	259_I	0.900	0.98
120_K	126_S	0.896	0.98
90_Y	113_V	0.895	0.98
198_Q	226_D	0.894	0.98
88_L	264_F	0.893	0.98
12_L	15_L	0.886	0.98
113_V	127_V	0.885	0.98
189_D	192_T	0.881	0.98
130_S	280_T	0.878	0.98
182_K	196_L	0.875	0.98
229_Y	291_L	0.874	0.98
209_Y	249_T	0.870	0.97
220_I	244_T	0.869	0.97
87_N	110_M	0.869	0.97
140_M	144_H	0.867	0.97
232_G	248_S	0.865	0.97
303_L	313_L	0.865	0.97
88_L	113_V	0.862	0.97
97_A	101_N	0.861	0.97
70_T	73_D	0.853	0.97
82_H	110_M	0.853	0.97
167_I	179_V	0.851	0.97
141_T	292_V	0.850	0.97
305_K	312_E	0.850	0.97
145_M	207_V	0.840	0.97
200_M	205_A	0.836	0.97
135_G	249_T	0.836	0.97
32_M	47_G	0.833	0.97
220_I	241_G	0.829	0.97
223_I	230_A	0.829	0.97
155_A	159_W	0.829	0.97
35_P	95_E	0.822	0.96
30_V	261_A	0.822	0.96
78_I	96_Y	0.818	0.96
36_D	40_D	0.807	0.96
238_S	286_G	0.806	0.96
149_N	206_D	0.806	0.96
133_A	277_D	0.802	0.96
98_E	101_N	0.796	0.96
32_M	51_L	0.795	0.96
100_F	124_V	0.795	0.96
167_I	181_T	0.791	0.96
281_G	308_N	0.789	0.96
7_M	11_V	0.787	0.95
153_V	211_A	0.784	0.95
148_T	204_G	0.782	0.95
302_K	305_K	0.778	0.95
51_L	55_Q	0.777	0.95
82_H	103_V	0.774	0.95
241_G	244_T	0.773	0.95
262_E	265_N	0.773	0.95
230_A	245_V	0.773	0.95
38_I	45_T	0.773	0.95
8_I	14_L	0.771	0.95
144_H	173_E	0.769	0.95
263_Q	266_K	0.767	0.95
295_D	298_Q	0.765	0.95
302_K	312_E	0.764	0.95
34_F	48_Y	0.760	0.95
114_I	117_A	0.759	0.95
212_G	216_N	0.758	0.94
295_D	299_R	0.758	0.94
28_E	87_N	0.756	0.94
156_S	213_D	0.755	0.94
101_N	121_A	0.755	0.94
53_N	56_S	0.752	0.94
231_I	247_T	0.750	0.94
129_F	251_Q	0.750	0.94
146_S	177_I	0.746	0.94
145_M	246_L	0.746	0.94
53_N	255_K	0.745	0.94
169_G	172_Y	0.744	0.94
170_A	179_V	0.742	0.94
111_E	264_F	0.742	0.94
195_K	199_K	0.741	0.94
234_V	251_Q	0.733	0.93
34_F	38_I	0.733	0.93
116_N	251_Q	0.732	0.93
54_I	60_V	0.730	0.93
276_Y	280_T	0.727	0.93
211_A	233_Y	0.720	0.93
141_T	231_I	0.718	0.93
136_F	169_G	0.718	0.93
26_K	87_N	0.716	0.93
288_F	291_L	0.715	0.93
247_T	287_T	0.715	0.93
46_K	254_D	0.714	0.93
137_F	278_L	0.714	0.93
8_I	11_V	0.713	0.92
78_I	82_H	0.710	0.92
143_A	174_N	0.709	0.92
47_G	253_V	0.709	0.92
18_C	23_F	0.708	0.92
48_Y	62_V	0.705	0.92
102_L	106_D	0.705	0.92
143_A	149_N	0.705	0.92
125_T	260_I	0.705	0.92
278_L	307_Y	0.704	0.92
7_M	13_L	0.704	0.92
158_T	185_D	0.704	0.92
210_P	219_V	0.703	0.92
41_L	240_L	0.701	0.92
136_F	140_M	0.701	0.92
154_I	197_Y	0.701	0.92
54_I	62_V	0.701	0.92
140_M	170_A	0.698	0.92
192_T	196_L	0.697	0.92
60_V	261_A	0.696	0.92
50_G	54_I	0.696	0.92
54_I	258_E	0.690	0.91
197_Y	201_K	0.689	0.91
221_Q	224_K	0.687	0.91
90_Y	261_A	0.686	0.91
29_K	87_N	0.680	0.91
35_P	93_G	0.678	0.90
131_G	251_Q	0.678	0.90
159_W	162_E	0.677	0.90
131_G	249_T	0.674	0.90
238_S	242_E	0.673	0.90
233_Y	251_Q	0.673	0.90
135_G	209_Y	0.669	0.90
150_Q	203_E	0.669	0.90
49_K	235_T	0.666	0.90
135_G	211_A	0.666	0.90
141_T	145_M	0.666	0.90
207_V	246_L	0.663	0.89
71_E	95_E	0.662	0.89
127_V	260_I	0.660	0.89
20_Q	23_F	0.655	0.89
115_S	253_V	0.653	0.89
58_Y	265_N	0.651	0.89
180_N	200_M	0.651	0.89
191_T	194_V	0.651	0.89
80_D	84_R	0.651	0.89
288_F	292_V	0.649	0.88
292_V	296_F	0.648	0.88
47_G	92_H	0.647	0.88
15_L	19_G	0.647	0.88
118_K	126_S	0.644	0.88
97_A	114_I	0.644	0.88
281_G	304_I	0.642	0.88
243_N	291_L	0.641	0.88
250_V	286_G	0.638	0.88
222_Q	226_D	0.638	0.88
168_K	171_K	0.638	0.88
224_K	244_T	0.638	0.88
86_V	110_M	0.636	0.87
65_K	77_A	0.633	0.87
149_N	176_D	0.632	0.87
109_D	122_D	0.632	0.87
260_I	263_Q	0.631	0.87
40_D	44_G	0.631	0.87
56_S	109_D	0.629	0.87
103_V	106_D	0.629	0.87
201_K	222_Q	0.629	0.87
245_V	248_S	0.629	0.87
101_N	119_A	0.627	0.87
163_V	183_Y	0.626	0.87
236_D	286_G	0.626	0.87
118_K	128_H	0.625	0.87
140_M	300_I	0.625	0.87
83_K	106_D	0.623	0.86
127_V	276_Y	0.623	0.86
196_L	200_M	0.620	0.86
290_P	297_Q	0.620	0.86
11_V	15_L	0.618	0.86
21_T	24_K	0.617	0.86
7_M	17_G	0.617	0.86
75_I	99_V	0.615	0.86
48_Y	51_L	0.613	0.85
177_I	181_T	0.612	0.85
164_D	168_K	0.610	0.85
292_V	297_Q	0.610	0.85
160_Q	163_V	0.609	0.85
40_D	45_T	0.608	0.85
145_M	229_Y	0.608	0.85
8_I	12_L	0.607	0.85
35_P	44_G	0.606	0.85
135_G	162_E	0.606	0.85
119_A	122_D	0.606	0.85
18_C	25_G	0.603	0.85
113_V	260_I	0.603	0.85
13_L	16_S	0.603	0.85
126_S	273_D	0.601	0.84
125_T	270_E	0.600	0.84
92_H	127_V	0.598	0.84
278_L	304_I	0.596	0.84
264_F	269_L	0.594	0.84
10_S	14_L	0.592	0.83
154_I	210_P	0.591	0.83
74_I	96_Y	0.591	0.83
153_V	163_V	0.589	0.83
255_K	258_E	0.587	0.83
63_Y	84_R	0.583	0.83
55_Q	60_V	0.583	0.83
287_T	291_L	0.582	0.82
163_V	181_T	0.581	0.82
38_I	52_L	0.581	0.82
259_I	280_T	0.580	0.82
151_V	177_I	0.579	0.82
198_Q	225_K	0.577	0.82
138_G	247_T	0.576	0.82
216_N	233_Y	0.573	0.81
49_K	254_D	0.571	0.81
141_T	144_H	0.570	0.81
20_Q	24_K	0.569	0.81
63_Y	81_F	0.568	0.81
14_L	18_C	0.562	0.80
107_Y	112_F	0.559	0.80
285_M	300_I	0.558	0.80
237_Q	240_L	0.558	0.80
78_I	112_F	0.558	0.80
277_D	282_V	0.554	0.79
111_E	125_T	0.553	0.79
166_F	209_Y	0.549	0.79
263_Q	270_E	0.548	0.79
166_F	169_G	0.547	0.78
193_A	218_P	0.546	0.78
214_G	217_V	0.544	0.78
296_F	300_I	0.544	0.78
188_D	215_Y	0.543	0.78
120_K	273_D	0.543	0.78
144_H	295_D	0.541	0.78
54_I	265_N	0.538	0.77
194_V	222_Q	0.538	0.77
172_Y	175_P	0.538	0.77
125_T	271_G	0.538	0.77
73_D	77_A	0.536	0.77
46_K	49_K	0.536	0.77
98_E	102_L	0.536	0.77
172_Y	306_T	0.533	0.77
157_F	187_W	0.533	0.77
247_T	288_F	0.533	0.77
89_L	112_F	0.532	0.76
238_S	243_N	0.531	0.76
298_Q	305_K	0.531	0.76
165_G	169_G	0.529	0.76
125_T	263_Q	0.528	0.76
35_P	92_H	0.528	0.76
97_A	119_A	0.527	0.76
193_A	216_N	0.526	0.76
170_A	173_E	0.526	0.76
171_K	175_P	0.525	0.76
276_Y	282_V	0.522	0.75
16_S	19_G	0.521	0.75
151_V	166_F	0.520	0.75
224_K	241_G	0.520	0.75
115_S	257_Y	0.520	0.75
128_H	275_Y	0.520	0.75
16_S	20_Q	0.519	0.75
29_K	63_Y	0.518	0.75
33_L	77_A	0.517	0.74
87_N	109_D	0.517	0.74
43_W	162_E	0.515	0.74
8_I	13_L	0.514	0.74
9_F	16_S	0.512	0.74
168_K	172_Y	0.511	0.74
146_S	151_V	0.510	0.73
191_T	195_K	0.509	0.73
141_T	296_F	0.507	0.73
212_G	215_Y	0.507	0.73
270_E	273_D	0.507	0.73
210_P	216_N	0.507	0.73
109_D	147_K	0.506	0.73
114_I	126_S	0.506	0.73
43_W	116_N	0.506	0.73
151_V	163_V	0.505	0.73
135_G	153_V	0.505	0.73
132_E	161_P	0.505	0.73
91_G	96_Y	0.504	0.73
119_A	124_V	0.503	0.72
221_Q	225_K	0.503	0.72
48_Y	55_Q	0.502	0.72
162_E	233_Y	0.502	0.72
81_F	89_L	0.500	0.72
243_N	290_P	0.500	0.72

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
4pevA	1	0.9117	100	0.377	Contact Map
4iilA	1	0.9148	100	0.399	Contact Map
3s99A	1	0.9054	100	0.41	Contact Map
4p98A	1	0.8991	100	0.414	Contact Map
2fqxA	1	0.9148	100	0.431	Contact Map
2hqbA	1	0.8864	100	0.435	Contact Map
4ycsA	1	0.3785	100	0.61	Contact Map
4wzzA	1	0.8675	99.9	0.713	Contact Map
4yo7A	1	0.8423	99.7	0.758	Contact Map
4z0nA	1	0.8486	99.7	0.762	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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