YFDC - ECOLI - GREMLIN Contacts

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YFDC - Inner membrane protein YfdC

UniProt:	P37327	Sequences: MDNDKIDQHSDEIEVESEEKERGKKIEIDEDRLPSRAMAIHEHIRQDGEKELERDAMALLWSAIAAGLSMGASLLAKGIFQVELEGVPGSFLLENLGYTFGFIIVIMARQQLFTENTVTAVLPVMQKPTMSNVGLLIRLWGVVLLGNILGTGIAAWAFEYMPIFNEETRDAFVKIGMDVMKNTPSEMFANAIISGWLIATMVWMFPAAGAAKIVVIILMTWLIALGDTTHIVVGSVEILYLVFNGTLHWSDFIWPFALPTLAGNICGGTFIFALMSHAQIRNDMSNKRKAEARQKAERAENIKKNYKNPA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12420
Length:	310 (248)
Sequences:	2133 (1416)
Seq/√Len:	89.9

ECOLI - YFDC FOCA FOCB NIRC
BACSU - YRHG YWCJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
188_F	266_C	7.403	1.00
188_F	262_A	4.751	1.00
63_A	146_G	4.000	1.00
210_A	214_V	3.966	1.00
187_M	260_T	3.841	1.00
124_V	133_V	3.774	1.00
262_A	266_C	3.252	1.00
64_I	153_I	3.226	1.00
60_L	146_G	3.095	1.00
144_L	261_L	3.093	1.00
71_G	154_A	3.036	1.00
184_P	259_P	2.730	1.00
241_L	244_N	2.606	1.00
76_A	222_L	2.603	1.00
48_G	123_P	2.448	1.00
238_I	252_F	2.446	1.00
113_F	117_T	2.305	1.00
60_L	142_V	2.288	1.00
196_W	271_I	2.235	1.00
156_W	160_Y	2.198	1.00
48_G	51_E	2.118	1.00
99_T	217_I	2.023	1.00
124_V	136_L	2.012	1.00
53_E	135_L	1.958	1.00
136_L	140_W	1.927	1.00
116_N	139_L	1.859	1.00
64_I	149_L	1.802	1.00
108_A	276_S	1.782	1.00
140_W	265_I	1.777	1.00
183_T	186_E	1.768	1.00
192_I	266_C	1.766	1.00
68_L	196_W	1.758	1.00
56_A	142_V	1.755	1.00
137_I	141_G	1.753	1.00
59_L	142_V	1.742	1.00
241_L	245_G	1.738	1.00
103_I	213_I	1.721	1.00
208_A	211_A	1.719	1.00
104_I	200_T	1.698	1.00
113_F	265_I	1.657	1.00
124_V	131_S	1.637	1.00
182_N	190_N	1.620	1.00
108_A	203_W	1.614	1.00
157_A	189_A	1.582	1.00
174_K	177_M	1.579	1.00
144_L	231_I	1.576	1.00
148_I	235_S	1.557	1.00
46_Q	128_P	1.539	1.00
60_L	64_I	1.506	1.00
35_S	43_H	1.503	1.00
87_V	90_S	1.495	1.00
123_P	131_S	1.489	1.00
248_H	251_D	1.477	1.00
41_H	281_R	1.469	1.00
77_K	94_E	1.463	0.99
117_T	140_W	1.460	0.99
231_I	261_L	1.436	0.99
72_A	196_W	1.409	0.99
242_V	249_W	1.408	0.99
60_L	149_L	1.406	0.99
92_L	221_W	1.396	0.99
185_S	189_A	1.393	0.99
265_I	269_T	1.373	0.99
271_I	275_M	1.369	0.99
40_I	207_A	1.364	0.99
134_G	138_R	1.361	0.99
76_A	221_W	1.356	0.99
204_M	215_V	1.344	0.99
100_F	222_L	1.304	0.99
36_R	39_A	1.304	0.99
182_N	187_M	1.293	0.99
80_F	93_L	1.291	0.99
177_M	181_K	1.269	0.99
253_I	258_L	1.248	0.98
133_V	137_I	1.244	0.98
132_N	135_L	1.237	0.98
78_G	175_I	1.227	0.98
95_N	225_L	1.226	0.98
62_S	279_Q	1.224	0.98
261_L	265_I	1.222	0.98
76_A	225_L	1.212	0.98
96_L	217_I	1.210	0.98
145_L	149_L	1.206	0.98
184_P	262_A	1.205	0.98
258_L	262_A	1.197	0.98
157_A	193_I	1.188	0.98
177_M	246_T	1.175	0.98
101_G	224_A	1.175	0.98
178_D	181_K	1.172	0.98
194_S	232_V	1.172	0.98
155_A	240_Y	1.170	0.98
44_I	206_P	1.162	0.97
81_Q	171_A	1.155	0.97
186_E	190_N	1.153	0.97
141_G	145_L	1.143	0.97
122_L	273_A	1.137	0.97
152_G	243_F	1.124	0.97
234_G	256_F	1.121	0.97
144_L	257_A	1.118	0.97
55_D	58_A	1.115	0.97
86_G	89_G	1.114	0.97
191_A	259_P	1.108	0.97
110_Q	276_S	1.095	0.96
270_F	274_L	1.090	0.96
65_A	275_M	1.077	0.96
75_L	226_G	1.072	0.96
74_L	237_E	1.071	0.96
106_I	216_I	1.069	0.96
171_A	174_K	1.063	0.96
68_L	71_G	1.058	0.95
49_E	128_P	1.050	0.95
62_S	111_Q	1.047	0.95
105_V	191_A	1.041	0.95
232_V	235_S	1.039	0.95
272_F	276_S	1.034	0.95
155_A	243_F	1.032	0.95
78_G	172_F	1.029	0.95
105_V	110_Q	1.021	0.95
184_P	188_F	1.016	0.94
148_I	152_G	1.015	0.94
56_A	60_L	1.014	0.94
191_A	261_L	0.997	0.94
103_I	218_L	0.997	0.94
240_Y	244_N	0.994	0.94
196_W	272_F	0.992	0.94
72_A	154_A	0.984	0.93
72_A	197_L	0.979	0.93
195_G	223_I	0.976	0.93
81_Q	94_E	0.970	0.93
96_L	221_W	0.964	0.93
251_D	255_P	0.960	0.93
231_I	257_A	0.950	0.92
126_Q	277_H	0.949	0.92
156_W	243_F	0.948	0.92
139_L	143_V	0.945	0.92
125_M	277_H	0.932	0.91
59_L	138_R	0.928	0.91
154_A	196_W	0.927	0.91
69_S	110_Q	0.924	0.91
172_F	240_Y	0.918	0.91
65_A	69_S	0.910	0.90
198_I	223_I	0.908	0.90
46_Q	50_K	0.906	0.90
161_M	193_I	0.892	0.89
184_P	255_P	0.888	0.89
179_V	195_G	0.886	0.89
39_A	42_E	0.879	0.89
179_V	233_V	0.870	0.88
104_I	197_L	0.863	0.88
179_V	234_G	0.857	0.88
255_P	259_P	0.856	0.87
57_M	278_A	0.856	0.87
82_V	171_A	0.856	0.87
125_M	274_L	0.847	0.87
203_W	276_S	0.844	0.87
190_N	229_T	0.843	0.87
107_M	207_A	0.832	0.86
43_H	206_P	0.830	0.86
259_P	262_A	0.829	0.86
108_A	204_M	0.827	0.86
113_F	232_V	0.826	0.86
165_N	186_E	0.826	0.86
59_L	143_V	0.826	0.86
78_G	236_V	0.826	0.86
133_V	136_L	0.824	0.85
113_F	261_L	0.824	0.85
69_S	276_S	0.818	0.85
179_V	223_I	0.818	0.85
170_D	174_K	0.809	0.84
135_L	138_R	0.805	0.84
49_E	53_E	0.804	0.84
35_S	39_A	0.799	0.84
152_G	155_A	0.796	0.83
144_L	148_I	0.795	0.83
85_E	88_P	0.795	0.83
152_G	239_L	0.793	0.83
184_P	187_M	0.791	0.83
52_L	131_S	0.784	0.82
187_M	191_A	0.778	0.82
106_I	202_V	0.777	0.82
45_R	126_Q	0.776	0.82
242_V	252_F	0.771	0.81
223_I	234_G	0.770	0.81
204_M	219_M	0.769	0.81
108_A	200_T	0.766	0.81
80_F	97_G	0.763	0.81
197_L	216_I	0.758	0.80
83_E	95_N	0.756	0.80
119_T	123_P	0.754	0.80
162_P	190_N	0.753	0.80
42_E	46_Q	0.752	0.80
127_K	133_V	0.748	0.79
62_S	203_W	0.744	0.79
96_L	103_I	0.743	0.79
281_R	284_M	0.741	0.79
117_T	121_V	0.740	0.79
201_M	223_I	0.739	0.79
56_A	141_G	0.737	0.78
268_G	273_A	0.737	0.78
196_W	200_T	0.736	0.78
111_Q	116_N	0.735	0.78
39_A	209_G	0.734	0.78
117_T	268_G	0.732	0.78
170_D	173_V	0.727	0.77
118_V	213_I	0.720	0.77
158_F	161_M	0.719	0.77
111_Q	143_V	0.713	0.76
160_Y	189_A	0.713	0.76
144_L	232_V	0.712	0.76
176_G	238_I	0.711	0.76
203_W	272_F	0.711	0.76
46_Q	49_E	0.711	0.76
238_I	242_V	0.710	0.76
246_T	251_D	0.710	0.76
100_F	104_I	0.708	0.76
161_M	189_A	0.706	0.75
153_I	156_W	0.702	0.75
143_V	203_W	0.697	0.74
195_G	220_T	0.697	0.74
69_S	104_I	0.695	0.74
103_I	216_I	0.692	0.74
61_W	275_M	0.689	0.74
49_E	131_S	0.687	0.73
63_A	143_V	0.687	0.73
114_T	194_S	0.684	0.73
53_E	247_L	0.682	0.73
113_F	144_L	0.676	0.72
37_A	280_I	0.675	0.72
77_K	81_Q	0.674	0.72
99_T	103_I	0.667	0.71
216_I	220_T	0.665	0.71
269_T	273_A	0.664	0.71
247_L	251_D	0.662	0.71
180_M	251_D	0.661	0.70
37_A	40_I	0.660	0.70
113_F	268_G	0.658	0.70
118_V	272_F	0.654	0.70
120_A	123_P	0.653	0.70
36_R	40_I	0.652	0.69
177_M	247_L	0.651	0.69
140_W	231_I	0.651	0.69
121_V	125_M	0.648	0.69
78_G	237_E	0.645	0.69
184_P	258_L	0.645	0.69
77_K	224_A	0.645	0.69
223_I	233_V	0.643	0.68
84_L	89_G	0.640	0.68
137_I	266_C	0.637	0.68
270_F	275_M	0.637	0.68
236_V	239_L	0.636	0.68
194_S	260_T	0.636	0.68
155_A	239_L	0.632	0.67
175_I	237_E	0.630	0.67
87_V	262_A	0.630	0.67
157_A	161_M	0.629	0.67
37_A	232_V	0.629	0.67
57_M	127_K	0.626	0.66
229_T	234_G	0.624	0.66
124_V	127_K	0.623	0.66
71_G	236_V	0.621	0.66
163_I	166_E	0.619	0.65
131_S	135_L	0.619	0.65
197_L	219_M	0.619	0.65
124_V	137_I	0.618	0.65
72_A	232_V	0.616	0.65
195_G	234_G	0.614	0.65
52_L	120_A	0.612	0.65
36_R	48_G	0.612	0.65
159_E	243_F	0.612	0.65
85_E	90_S	0.609	0.64
257_A	260_T	0.604	0.64
42_E	45_R	0.602	0.63
51_E	236_V	0.601	0.63
174_K	178_D	0.601	0.63
84_L	90_S	0.599	0.63
231_I	260_T	0.588	0.61
113_F	231_I	0.586	0.61
213_I	218_L	0.585	0.61
198_I	220_T	0.584	0.61
188_F	191_A	0.583	0.61
163_I	190_N	0.582	0.61
74_L	77_K	0.582	0.61
119_T	131_S	0.580	0.60
145_L	253_I	0.576	0.60
158_F	193_I	0.575	0.60
211_A	214_V	0.574	0.60
73_S	101_G	0.572	0.59
97_G	221_W	0.572	0.59
64_I	271_I	0.571	0.59
276_S	280_I	0.570	0.59
124_V	135_L	0.570	0.59
177_M	180_M	0.568	0.59
66_A	115_E	0.568	0.59
141_G	258_L	0.567	0.59
73_S	95_N	0.567	0.59
45_R	281_R	0.566	0.59
35_S	46_Q	0.565	0.58
151_T	235_S	0.564	0.58
35_S	209_G	0.564	0.58
84_L	87_V	0.564	0.58
180_M	247_L	0.564	0.58
242_V	245_G	0.561	0.58
47_D	50_K	0.560	0.58
162_P	186_E	0.559	0.58
195_G	233_V	0.558	0.58
45_R	48_G	0.557	0.57
43_H	47_D	0.555	0.57
187_M	255_P	0.554	0.57
167_E	170_D	0.553	0.57
161_M	190_N	0.551	0.57
217_I	220_T	0.551	0.57
57_M	282_N	0.550	0.56
86_G	90_S	0.550	0.56
62_S	110_Q	0.549	0.56
99_T	220_T	0.547	0.56
34_P	37_A	0.547	0.56
154_A	232_V	0.545	0.56
74_L	236_V	0.545	0.56
62_S	105_V	0.545	0.56
98_Y	223_I	0.545	0.56
199_A	229_T	0.542	0.55
229_T	256_F	0.542	0.55
93_L	140_W	0.541	0.55
250_S	255_P	0.539	0.55
115_E	178_D	0.537	0.55
60_L	132_N	0.536	0.55
113_F	121_V	0.535	0.54
54_R	59_L	0.535	0.54
40_I	203_W	0.534	0.54
257_A	261_L	0.534	0.54
243_F	249_W	0.531	0.54
52_L	139_L	0.530	0.54
41_H	203_W	0.530	0.54
203_W	280_I	0.528	0.53
168_T	190_N	0.528	0.53
118_V	280_I	0.528	0.53
239_L	242_V	0.527	0.53
61_W	279_Q	0.527	0.53
199_A	235_S	0.525	0.53
47_D	51_E	0.524	0.53
59_L	116_N	0.524	0.53
178_D	183_T	0.522	0.53
106_I	205_F	0.521	0.52
83_E	86_G	0.520	0.52
207_A	280_I	0.520	0.52
137_I	140_W	0.520	0.52
108_A	207_A	0.520	0.52
223_I	256_F	0.519	0.52
42_E	128_P	0.519	0.52
42_E	149_L	0.518	0.52
253_I	259_P	0.517	0.52
41_H	122_L	0.516	0.52
104_I	151_T	0.516	0.52
170_D	248_H	0.515	0.52
76_A	190_N	0.515	0.52
97_G	108_A	0.514	0.52
127_K	132_N	0.514	0.52
72_A	119_T	0.512	0.51
148_I	253_I	0.511	0.51
111_Q	139_L	0.510	0.51
255_P	258_L	0.509	0.51
84_L	93_L	0.509	0.51
101_G	143_V	0.507	0.51
138_R	155_A	0.506	0.50
60_L	191_A	0.506	0.50
64_I	68_L	0.504	0.50
102_F	118_V	0.503	0.50
171_A	175_I	0.502	0.50
95_N	224_A	0.502	0.50
112_L	268_G	0.502	0.50
187_M	259_P	0.501	0.50
56_A	138_R	0.500	0.50

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
3kcuA	3	0.729	100	0.229	Contact Map
3klyA	3	0.7452	100	0.233	Contact Map
3tdsE	3	0.8226	100	0.257	Contact Map
4fc4A	3	0.7806	100	0.266	Contact Map
3iyzA	3	0.6613	96.2	0.926	Contact Map
3zojA	3	0.7903	95.9	0.928	Contact Map
3llqA	3	0.7258	94	0.936	Contact Map
2b6oA	6	0.7032	93.5	0.937	Contact Map
2zz9A	3	0.6613	93	0.938	Contact Map
4oj2X	3	0.7355	92.1	0.94	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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