YjgP_YjgQ - PFAM28P - GREMLIN Contacts

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YjgP_YjgQ - Predicted permease YjgP/YjgQ family

PFAM:	PF03739	Sequences: RYILREFLGPFLLVLLVLLFILLLFDLLELLDDLVGGGLPLGVVLEYLLLLLPSILYLLLPLAVLLAVLLTLGRLARDSELTAMRASGISLWRLLRPVLILALLLSLLSFLLSEYVVPWANRKARELLAEIRGKKPALLIKPGVFLRDGDGRVIYVESVDPDGGTLRGVFIYDFDRDGGLVRVITAESARLDSDPDDGRWVLEDGTIYEFDPGGPEYRITRFDEYDLPLDLTPEDLRRSDKDPEEMSLWELRRYIRRLKSSGLDARRYRVELHKRLALPLACLVLALLAAPLGLRSRRGGRGLGIGIGILLGFLYYLLLSLGEALGESGVLPPLLAAWLPNLLFLLLGLYLLRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	354 (353)
Sequences:	49994 (35940)
Seq/√Len:	1912.9
META:	0.884

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_E	168_G	4.790	1.00
205_G	222_F	4.601	1.00
187_E	204_D	4.512	1.00
188_S	203_E	4.255	1.00
173_D	182_R	3.734	1.00
158_S	167_R	3.456	1.00
273_H	338_W	3.384	1.00
72_L	98_V	3.301	1.00
165_T	188_S	3.193	1.00
259_K	269_R	2.985	1.00
192_D	201_V	2.885	1.00
74_R	78_D	2.706	1.00
182_R	207_I	2.701	1.00
123_K	126_E	2.687	1.00
190_R	203_E	2.659	1.00
5_R	9_G	2.641	1.00
201_V	224_E	2.634	1.00
201_V	226_D	2.534	1.00
11_F	67_A	2.455	1.00
175_D	179_G	2.327	1.00
95_L	290_A	2.317	1.00
4_L	101_L	2.296	1.00
199_R	226_D	2.219	1.00
252_R	272_L	2.215	1.00
102_A	286_A	2.184	1.00
182_R	209_E	2.135	1.00
111_L	115_Y	2.132	1.00
326_G	336_A	2.117	1.00
274_K	323_E	2.094	1.00
152_R	173_D	2.089	1.00
93_R	96_R	2.061	1.00
67_A	71_T	2.052	1.00
203_E	224_E	2.050	1.00
160_D	163_G	1.994	1.00
279_P	282_C	1.990	1.00
119_W	123_K	1.974	1.00
160_D	167_R	1.960	1.00
271_E	275_R	1.923	1.00
209_E	218_R	1.862	1.00
271_E	274_K	1.861	1.00
42_G	46_E	1.846	1.00
298_R	301_R	1.846	1.00
206_T	221_R	1.841	1.00
15_L	56_L	1.831	1.00
189_A	202_L	1.827	1.00
167_R	188_S	1.825	1.00
10_P	71_T	1.791	1.00
40_P	43_V	1.776	1.00
265_A	269_R	1.766	1.00
6_E	74_R	1.718	1.00
204_D	223_D	1.714	1.00
247_S	250_E	1.696	1.00
192_D	197_D	1.682	1.00
43_V	46_E	1.681	1.00
165_T	190_R	1.673	1.00
190_R	201_V	1.666	1.00
92_W	96_R	1.666	1.00
45_L	49_L	1.661	1.00
277_A	338_W	1.653	1.00
107_L	111_L	1.601	1.00
15_L	63_A	1.557	1.00
166_L	189_A	1.552	1.00
84_M	94_L	1.544	1.00
84_M	89_I	1.538	1.00
184_I	207_I	1.537	1.00
103_L	107_L	1.508	1.00
60_L	109_S	1.504	1.00
64_V	282_C	1.503	1.00
19_L	52_L	1.494	1.00
64_V	105_L	1.489	1.00
298_R	303_L	1.483	1.00
349_L	353_R	1.478	1.00
46_E	50_L	1.477	1.00
169_V	189_A	1.475	1.00
207_I	220_T	1.475	1.00
323_E	327_E	1.474	1.00
142_P	158_S	1.473	1.00
106_S	283_L	1.471	1.00
112_L	116_V	1.452	1.00
79_S	82_T	1.449	1.00
57_Y	113_S	1.449	1.00
297_R	302_G	1.447	1.00
1_R	5_R	1.442	1.00
298_R	302_G	1.440	1.00
126_E	130_E	1.435	1.00
156_V	166_L	1.422	1.00
110_F	114_E	1.411	1.00
284_V	348_G	1.410	1.00
186_A	202_L	1.408	1.00
208_Y	217_Y	1.408	1.00
168_G	187_E	1.404	1.00
41_L	45_L	1.386	1.00
338_W	341_N	1.385	1.00
96_R	100_I	1.383	1.00
281_A	315_Y	1.371	1.00
68_V	286_A	1.364	1.00
297_R	301_R	1.360	1.00
34_L	44_V	1.358	1.00
346_L	350_Y	1.357	1.00
49_L	53_P	1.351	1.00
191_L	233_P	1.340	1.00
342_L	346_L	1.332	1.00
284_V	344_F	1.323	1.00
331_L	336_A	1.295	1.00
209_E	220_T	1.286	1.00
252_R	256_R	1.282	1.00
207_I	225_Y	1.282	1.00
266_R	269_R	1.280	1.00
122_R	126_E	1.271	1.00
47_Y	124_A	1.268	1.00
50_L	123_K	1.264	1.00
26_D	30_L	1.235	1.00
248_L	272_L	1.227	1.00
125_R	128_L	1.220	1.00
63_A	67_A	1.214	1.00
98_V	286_A	1.213	1.00
83_A	87_S	1.208	1.00
248_L	275_R	1.206	1.00
232_T	235_D	1.205	1.00
188_S	204_D	1.181	1.00
173_D	176_R	1.170	1.00
199_R	228_P	1.165	1.00
119_W	122_R	1.162	1.00
50_L	120_A	1.162	1.00
332_P	335_L	1.162	1.00
103_L	283_L	1.150	1.00
272_L	276_L	1.146	1.00
273_H	334_L	1.139	1.00
125_R	245_E	1.136	1.00
246_M	250_E	1.132	1.00
6_E	9_G	1.130	1.00
284_V	345_L	1.124	1.00
46_E	123_K	1.123	1.00
169_V	202_L	1.122	1.00
69_L	308_G	1.118	1.00
7_F	71_T	1.115	1.00
8_L	12_L	1.114	1.00
6_E	75_L	1.109	1.00
211_D	214_G	1.104	1.00
104_L	107_L	1.090	1.00
269_R	273_H	1.090	1.00
241_K	250_E	1.088	1.00
194_D	197_D	1.087	1.00
54_S	58_L	1.086	1.00
26_D	48_L	1.083	1.00
322_G	336_A	1.080	1.00
342_L	345_L	1.074	1.00
315_Y	341_N	1.072	1.00
259_K	265_A	1.060	1.00
256_R	259_K	1.055	1.00
116_V	119_W	1.048	1.00
76_A	81_L	1.038	1.00
128_L	132_R	1.035	1.00
51_L	124_A	1.031	1.00
83_A	86_A	1.025	1.00
103_L	106_S	1.024	1.00
192_D	199_R	1.021	1.00
160_D	164_G	1.019	1.00
109_S	282_C	1.016	1.00
117_V	120_A	1.014	1.00
152_R	171_I	1.005	1.00
100_I	104_L	1.002	1.00
64_V	286_A	0.997	1.00
166_L	169_V	0.997	1.00
75_L	84_M	0.994	1.00
3_I	75_L	0.993	1.00
14_V	66_L	0.987	1.00
334_L	342_L	0.986	1.00
204_D	221_R	0.984	1.00
246_M	254_Y	0.981	1.00
124_A	128_L	0.979	1.00
248_L	276_L	0.979	1.00
173_D	181_V	0.970	1.00
297_R	304_G	0.970	1.00
316_Y	320_S	0.968	1.00
65_L	289_A	0.965	1.00
7_F	98_V	0.962	1.00
111_L	116_V	0.961	1.00
277_A	341_N	0.959	1.00
320_S	324_A	0.958	1.00
116_V	120_A	0.957	1.00
18_L	59_L	0.957	1.00
256_R	260_S	0.956	1.00
254_Y	258_L	0.955	1.00
206_T	219_I	0.953	1.00
62_L	312_G	0.952	1.00
160_D	165_T	0.949	1.00
57_Y	117_V	0.944	1.00
332_P	336_A	0.943	1.00
297_R	303_L	0.937	1.00
81_L	294_L	0.937	1.00
255_I	272_L	0.935	1.00
252_R	255_I	0.932	1.00
211_D	216_E	0.931	1.00
170_F	183_V	0.930	1.00
336_A	340_P	0.929	1.00
30_L	34_L	0.929	1.00
43_V	127_L	0.925	1.00
115_Y	118_P	0.925	1.00
42_G	45_L	0.923	1.00
104_L	108_L	0.923	1.00
339_L	343_L	0.920	1.00
159_V	166_L	0.919	1.00
255_I	265_A	0.916	1.00
255_I	269_R	0.914	1.00
314_L	344_F	0.912	1.00
43_V	131_I	0.909	1.00
11_F	60_L	0.906	1.00
258_L	261_S	0.906	1.00
19_L	59_L	0.906	1.00
115_Y	249_W	0.904	1.00
76_A	293_G	0.903	1.00
270_V	337_A	0.896	1.00
322_G	339_L	0.894	1.00
262_G	265_A	0.894	1.00
108_L	112_L	0.893	1.00
107_L	110_F	0.893	1.00
46_E	127_L	0.891	1.00
106_S	282_C	0.888	1.00
255_I	259_K	0.886	1.00
170_F	185_T	0.884	1.00
322_G	325_L	0.883	1.00
184_I	225_Y	0.879	1.00
114_E	248_L	0.878	1.00
276_L	279_P	0.874	1.00
53_P	57_Y	0.873	1.00
145_F	155_Y	0.870	1.00
222_F	225_Y	0.870	1.00
273_H	276_L	0.870	1.00
11_F	105_L	0.870	1.00
288_L	348_G	0.869	1.00
2_Y	6_E	0.862	1.00
270_V	326_G	0.859	1.00
85_R	91_L	0.856	1.00
115_Y	119_W	0.855	1.00
322_G	340_P	0.854	1.00
312_G	316_Y	0.854	1.00
7_F	101_L	0.853	1.00
255_I	258_L	0.851	1.00
320_S	323_E	0.849	1.00
191_L	200_W	0.848	1.00
53_P	56_L	0.847	1.00
23_L	48_L	0.845	1.00
220_T	225_Y	0.842	1.00
184_I	205_G	0.839	1.00
26_D	29_E	0.836	1.00
72_L	290_A	0.836	1.00
130_E	134_K	0.835	1.00
106_S	110_F	0.834	1.00
300_G	304_G	0.832	1.00
64_V	101_L	0.829	1.00
310_L	314_L	0.828	1.00
210_F	217_Y	0.826	1.00
128_L	131_I	0.825	1.00
266_R	329_G	0.825	1.00
114_E	275_R	0.825	1.00
99_L	102_A	0.823	1.00
127_L	131_I	0.821	1.00
293_G	296_S	0.820	1.00
7_F	64_V	0.820	1.00
114_E	276_L	0.819	1.00
345_L	348_G	0.814	1.00
68_V	289_A	0.813	1.00
97_P	100_I	0.812	1.00
125_R	129_A	0.806	1.00
345_L	349_L	0.806	1.00
10_P	14_V	0.804	1.00
274_K	319_L	0.804	1.00
105_L	282_C	0.803	1.00
124_A	127_L	0.801	1.00
19_L	56_L	0.800	1.00
30_L	48_L	0.798	1.00
102_A	106_S	0.797	1.00
335_L	342_L	0.796	1.00
318_L	322_G	0.796	1.00
259_K	262_G	0.795	1.00
316_Y	319_L	0.795	1.00
171_I	202_L	0.794	1.00
25_F	29_E	0.791	1.00
168_G	185_T	0.791	1.00
22_L	55_I	0.789	1.00
71_T	75_L	0.789	1.00
56_L	60_L	0.786	1.00
273_H	277_A	0.786	1.00
280_L	341_N	0.783	1.00
254_Y	257_R	0.780	1.00
2_Y	84_M	0.779	1.00
147_R	153_V	0.777	1.00
180_L	209_E	0.776	1.00
13_L	17_V	0.772	1.00
287_L	348_G	0.770	1.00
60_L	63_A	0.769	1.00
314_L	318_L	0.769	1.00
211_D	218_R	0.769	1.00
298_R	304_G	0.765	1.00
324_A	328_S	0.764	1.00
253_R	257_R	0.763	1.00
100_I	103_L	0.760	1.00
319_L	323_E	0.760	1.00
301_R	304_G	0.758	1.00
9_G	13_L	0.758	1.00
51_L	54_S	0.758	1.00
95_L	99_L	0.756	1.00
258_L	262_G	0.755	1.00
175_D	181_V	0.753	1.00
14_V	18_L	0.749	1.00
46_E	49_L	0.748	1.00
202_L	205_G	0.746	1.00
292_L	296_S	0.746	1.00
64_V	68_V	0.745	1.00
260_S	263_L	0.740	1.00
54_S	121_N	0.740	1.00
120_A	123_K	0.738	1.00
205_G	223_D	0.738	1.00
317_L	321_L	0.737	1.00
12_L	16_L	0.734	1.00
299_G	302_G	0.733	1.00
270_V	327_E	0.732	1.00
89_I	93_R	0.731	1.00
108_L	111_L	0.729	1.00
22_L	59_L	0.729	1.00
92_W	352_L	0.726	1.00
10_P	67_A	0.725	1.00
192_D	198_G	0.722	1.00
207_I	222_F	0.718	1.00
254_Y	268_Y	0.715	1.00
185_T	206_T	0.712	1.00
257_R	261_S	0.712	1.00
14_V	17_V	0.712	1.00
16_L	20_F	0.711	1.00
248_L	252_R	0.710	1.00
51_L	55_I	0.710	1.00
258_L	263_L	0.708	1.00
192_D	226_D	0.706	1.00
23_L	52_L	0.706	1.00
333_P	337_A	0.704	1.00
159_V	164_G	0.704	1.00
257_R	260_S	0.704	1.00
344_F	348_G	0.704	1.00
331_L	335_L	0.703	1.00
213_G	216_E	0.697	1.00
7_F	68_V	0.695	1.00
337_A	341_N	0.695	1.00
315_Y	344_F	0.692	1.00
350_Y	353_R	0.690	1.00
187_E	205_G	0.686	1.00
174_F	180_L	0.685	1.00
106_S	279_P	0.685	1.00
47_Y	51_L	0.683	1.00
81_L	94_L	0.682	1.00
185_T	208_Y	0.680	1.00
29_E	32_D	0.679	1.00
90_S	93_R	0.675	1.00
39_L	43_V	0.675	1.00
70_L	74_R	0.674	1.00
95_L	352_L	0.674	1.00
329_G	336_A	0.672	1.00
60_L	105_L	0.671	1.00
56_L	112_L	0.670	1.00
336_A	339_L	0.670	1.00
117_V	121_N	0.669	1.00
143_G	155_Y	0.668	1.00
114_E	249_W	0.667	1.00
4_L	7_F	0.666	1.00
191_L	198_G	0.664	1.00
127_L	130_E	0.662	1.00
4_L	8_L	0.662	1.00
241_K	245_E	0.660	1.00
281_A	341_N	0.658	1.00
255_I	262_G	0.656	1.00
291_P	348_G	0.655	1.00
260_S	264_D	0.655	1.00
7_F	11_F	0.654	1.00
300_G	303_L	0.654	1.00
315_Y	319_L	0.650	1.00
211_D	215_P	0.648	1.00
14_V	70_L	0.648	1.00
140_I	145_F	0.648	1.00
287_L	291_P	0.648	1.00
311_L	344_F	0.647	1.00
25_F	28_L	0.646	1.00
18_L	63_A	0.644	1.00
32_D	36_G	0.641	1.00
26_D	51_L	0.640	1.00
335_L	339_L	0.640	1.00
81_L	84_M	0.640	1.00
6_E	71_T	0.639	1.00
231_L	236_L	0.637	1.00
337_A	340_P	0.634	1.00
7_F	67_A	0.633	1.00
184_I	202_L	0.632	1.00
299_G	303_L	0.631	1.00
141_K	144_V	0.630	1.00
65_L	312_G	0.630	1.00
270_V	274_K	0.629	1.00
271_E	327_E	0.628	1.00
167_R	187_E	0.628	1.00
248_L	251_L	0.628	1.00
15_L	19_L	0.627	1.00
87_S	91_L	0.627	1.00
54_S	57_Y	0.625	1.00
177_D	180_L	0.624	1.00
318_L	340_P	0.623	1.00
75_L	81_L	0.623	1.00
9_G	12_L	0.621	1.00
86_A	89_I	0.619	1.00
20_F	24_L	0.617	1.00
154_I	171_I	0.616	1.00
171_I	184_I	0.612	1.00
297_R	300_G	0.611	1.00
11_F	101_L	0.610	1.00
2_Y	5_R	0.609	1.00
223_D	226_D	0.604	1.00
111_L	114_E	0.604	1.00
147_R	150_D	0.603	1.00
306_G	310_L	0.601	1.00
341_N	345_L	0.597	1.00
172_Y	180_L	0.596	1.00
129_A	133_G	0.594	1.00
335_L	338_W	0.592	1.00
109_S	112_L	0.591	1.00
14_V	67_A	0.589	1.00
91_L	294_L	0.589	1.00
59_L	63_A	0.588	1.00
22_L	26_D	0.588	1.00
326_G	329_G	0.587	1.00
249_W	253_R	0.586	1.00
288_L	311_L	0.585	1.00
319_L	322_G	0.585	1.00
265_A	268_Y	0.584	1.00
39_L	131_I	0.582	1.00
164_G	190_R	0.581	1.00
96_R	107_L	0.581	1.00
31_L	35_V	0.581	1.00
331_L	339_L	0.580	1.00
277_A	337_A	0.579	1.00
261_S	264_D	0.579	1.00
296_S	299_G	0.577	1.00
114_E	247_S	0.577	1.00
66_L	70_L	0.576	1.00
325_L	330_V	0.576	1.00
253_R	256_R	0.574	1.00
285_L	312_G	0.574	1.00
303_L	306_G	0.573	1.00
121_N	125_R	0.571	1.00
162_D	165_T	0.571	1.00
30_L	33_D	0.569	1.00
172_Y	183_V	0.569	1.00
4_L	104_L	0.568	1.00
100_I	107_L	0.567	1.00
22_L	48_L	0.565	1.00
3_I	84_M	0.564	1.00
2_Y	75_L	0.564	1.00
299_G	304_G	0.563	1.00
176_R	181_V	0.563	1.00
309_I	312_G	0.561	1.00
123_K	127_L	0.559	1.00
164_G	188_S	0.558	1.00
205_G	225_Y	0.557	1.00
282_C	286_A	0.557	1.00
145_F	172_Y	0.556	1.00
170_F	174_F	0.554	1.00
268_Y	272_L	0.554	1.00
295_R	304_G	0.553	1.00
200_W	233_P	0.553	1.00
112_L	117_V	0.552	1.00
99_L	103_L	0.551	1.00
193_S	197_D	0.549	1.00
110_F	276_L	0.549	1.00
156_V	159_V	0.545	1.00
212_P	215_P	0.545	1.00
339_L	346_L	0.545	1.00
146_L	149_G	0.544	1.00
64_V	67_A	0.543	1.00
326_G	337_A	0.542	1.00
53_P	120_A	0.540	1.00
82_T	85_R	0.540	1.00
65_L	285_L	0.539	1.00
244_E	271_E	0.539	1.00
91_L	290_A	0.538	1.00
343_L	346_L	0.537	1.00
26_D	55_I	0.537	1.00
161_P	164_G	0.536	1.00
55_I	58_L	0.536	1.00
29_E	33_D	0.536	1.00
343_L	347_L	0.535	1.00
333_P	336_A	0.535	1.00
76_A	294_L	0.534	1.00
71_T	98_V	0.530	1.00
110_F	279_P	0.530	1.00
319_L	337_A	0.530	1.00
339_L	342_L	0.529	1.00
216_E	219_I	0.529	1.00
317_L	320_S	0.529	1.00
281_A	285_L	0.526	1.00
280_L	338_W	0.525	1.00
32_D	35_V	0.525	1.00
102_A	283_L	0.524	1.00
144_V	147_R	0.522	1.00
23_L	26_D	0.522	1.00
132_R	135_K	0.521	1.00
142_P	145_F	0.520	1.00
96_R	99_L	0.518	1.00
18_L	62_L	0.517	1.00
106_S	280_L	0.517	1.00
4_L	100_I	0.516	1.00
173_D	178_G	0.515	1.00
72_L	94_L	0.515	1.00
143_G	157_E	0.515	1.00
280_L	284_V	0.513	1.00
243_P	268_Y	0.513	1.00
197_D	228_P	0.511	1.00
334_L	338_W	0.511	1.00
334_L	337_A	0.510	1.00
284_V	341_N	0.510	1.00
7_F	72_L	0.509	1.00
285_L	288_L	0.509	1.00
27_L	31_L	0.509	1.00
173_D	184_I	0.508	1.00
145_F	148_D	0.507	1.00
284_V	315_Y	0.506	1.00
11_F	64_V	0.506	1.00
44_V	48_L	0.506	1.00
347_L	350_Y	0.506	1.00
291_P	294_L	0.504	1.00
19_L	55_I	0.504	1.00
186_A	205_G	0.504	1.00
153_V	174_F	0.503	1.00
234_E	237_R	0.502	1.00
53_P	59_L	0.500	1.00

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
2m6bA	1	0.2458	4.8	0.96	Contact Map
4a18M	1	0.0932	4.2	0.961	Contact Map
4httA	1	0.2316	3.4	0.962	Contact Map
4us3A	1	0.2768	3.2	0.963	Contact Map
1oedC	1	0.2316	3	0.963	Contact Map
1oedE	1	0.2345	3	0.963	Contact Map
4cadC	1	0.1497	2.5	0.965	Contact Map
1oedB	1	0.2316	2.5	0.965	Contact Map
2llyA	1	0.2373	2.5	0.965	Contact Map
2kncA	1	0.1525	2.4	0.965	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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