IcmF-related - PFAM28P - GREMLIN Contacts

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IcmF-related - Intracellular multiplication and human macrophage-killing

PFAM:	PF06761	Sequences: LPALDALRDLPAGLYGYRRDGAPWSLRFGLYQGDKLGAAARAAYFRALRRLLLPRLAARLEEQLRALPAAPDPEALYEALKAYLMLGDPEHLDAAFLKAWLARDWQRALPGDAGAQQREALLAHLAALLALPPAIPPLSPLDAALVAQARATLRRLPLAERVYQRLKAEAAAAALPDFTLADALGPDAALVFTRSSPLSEGVPGLFTRDGYEEVFLPAIDEAAKQLAGEDDWVLGDSAAAASEADPAALAADLRRLYFADYIAAWDAFLNDLRVVPFASLADAADVLRLLSGPDSPLLALLRAVARNTT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	309 (304)
Sequences:	4500 (3417)
Seq/√Len:	196.0
META:	0.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
163_Y	260_D	5.235	1.00
209_D	213_E	4.420	1.00
208_R	212_E	3.755	1.00
84_L	150_R	3.497	1.00
98_K	126_A	3.470	1.00
82_A	97_L	3.080	1.00
269_L	304_V	2.957	1.00
196_S	271_D	2.919	1.00
178_F	303_A	2.852	1.00
32_Q	35_K	2.784	1.00
5_D	120_A	2.742	1.00
277_F	286_V	2.710	1.00
277_F	283_A	2.569	1.00
160_E	256_L	2.553	1.00
61_E	142_D	2.453	1.00
179_T	182_D	2.403	1.00
159_A	252_D	2.382	1.00
206_F	260_D	2.356	1.00
84_L	146_V	2.337	1.00
59_R	104_D	2.321	1.00
88_D	91_H	2.306	1.00
248_A	252_D	2.293	1.00
167_K	260_D	2.275	1.00
137_P	140_P	2.244	1.00
22_A	27_R	2.217	1.00
143_A	147_A	2.215	1.00
272_L	300_L	2.214	1.00
65_R	142_D	2.162	1.00
82_A	96_F	2.136	1.00
124_H	128_L	2.098	1.00
259_A	263_A	2.065	1.00
303_A	307_N	2.025	1.00
7_L	47_A	2.020	1.00
258_F	262_I	2.002	1.00
263_A	267_A	1.995	1.00
194_R	271_D	1.972	1.00
220_D	250_A	1.859	1.00
145_L	149_A	1.852	1.00
177_D	201_G	1.844	1.00
111_G	118_R	1.763	1.00
10_L	13_G	1.759	1.00
178_F	183_A	1.750	1.00
64_L	149_A	1.747	1.00
278_A	282_D	1.739	1.00
245_D	248_A	1.728	1.00
82_A	100_W	1.705	1.00
5_D	9_D	1.702	1.00
85_M	93_D	1.701	1.00
147_A	151_A	1.677	1.00
255_R	259_A	1.666	1.00
72_D	75_A	1.659	1.00
298_L	302_R	1.650	1.00
167_K	206_F	1.635	1.00
282_D	286_V	1.629	1.00
163_Y	167_K	1.601	1.00
56_L	101_L	1.597	1.00
112_D	115_A	1.594	1.00
15_Y	18_R	1.591	1.00
193_T	275_V	1.588	1.00
290_L	297_L	1.574	1.00
57_A	61_E	1.558	1.00
61_E	65_R	1.531	1.00
279_S	282_D	1.529	1.00
224_K	228_G	1.528	1.00
77_Y	229_E	1.504	1.00
114_G	117_Q	1.493	1.00
176_P	204_G	1.479	1.00
203_P	264_A	1.470	1.00
41_R	45_F	1.461	1.00
217_P	221_E	1.458	1.00
138_L	141_L	1.451	1.00
16_G	20_D	1.445	1.00
252_D	255_R	1.440	1.00
121_L	124_H	1.435	1.00
115_A	118_R	1.433	1.00
190_L	285_D	1.433	1.00
193_T	273_R	1.427	1.00
167_K	205_L	1.406	1.00
92_L	97_L	1.400	1.00
184_L	188_A	1.400	1.00
52_L	105_W	1.393	1.00
81_K	96_F	1.390	1.00
256_L	260_D	1.380	1.00
13_G	16_G	1.368	1.00
124_H	127_A	1.367	1.00
113_A	116_Q	1.366	1.00
300_L	304_V	1.364	1.00
175_L	204_G	1.361	1.00
179_T	201_G	1.353	1.00
281_A	285_D	1.332	1.00
211_Y	258_F	1.320	1.00
257_Y	261_Y	1.315	1.00
218_A	221_E	1.307	1.00
44_Y	124_H	1.302	1.00
93_D	96_F	1.298	1.00
22_A	31_Y	1.298	1.00
17_Y	20_D	1.287	1.00
63_Q	79_A	1.282	1.00
275_V	282_D	1.277	1.00
69_A	72_D	1.257	1.00
126_A	130_A	1.257	1.00
162_V	222_A	1.241	1.00
18_R	34_D	1.239	1.00
59_R	62_E	1.237	1.00
201_G	271_D	1.229	1.00
102_A	122_L	1.225	1.00
9_D	12_A	1.213	1.00
23_P	26_L	1.209	1.00
119_E	123_A	1.196	1.00
280_L	284_A	1.174	1.00
262_I	266_D	1.171	1.00
61_E	83_Y	1.168	1.00
5_D	8_R	1.161	1.00
159_A	256_L	1.158	1.00
80_L	84_L	1.158	1.00
170_A	214_V	1.155	1.00
144_A	147_A	1.154	1.00
85_M	92_L	1.150	1.00
44_Y	48_L	1.146	1.00
254_R	258_F	1.146	1.00
77_Y	81_K	1.142	1.00
8_R	12_A	1.141	1.00
111_G	117_Q	1.141	1.00
11_P	15_Y	1.137	1.00
96_F	100_W	1.130	1.00
285_D	288_R	1.127	1.00
84_L	232_W	1.119	1.00
105_W	125_L	1.108	1.00
26_L	33_G	1.101	1.00
60_L	79_A	1.099	1.00
282_D	285_D	1.098	1.00
195_S	271_D	1.091	1.00
192_F	272_L	1.080	1.00
109_L	112_D	1.078	1.00
303_A	306_R	1.076	1.00
7_L	10_L	1.076	1.00
16_G	19_R	1.074	1.00
79_A	100_W	1.074	1.00
81_K	233_V	1.073	1.00
61_E	145_L	1.073	1.00
194_R	198_L	1.060	1.00
48_L	53_L	1.060	1.00
111_G	115_A	1.049	1.00
164_Q	168_A	1.044	1.00
219_I	250_A	1.037	1.00
202_V	264_A	1.037	1.00
77_Y	150_R	1.037	1.00
39_A	42_A	1.027	1.00
209_D	307_N	1.026	1.00
85_M	91_H	1.012	1.00
210_G	215_F	1.009	1.00
122_L	126_A	1.009	1.00
144_A	148_Q	1.005	1.00
111_G	114_G	1.002	1.00
73_P	156_L	0.998	1.00
45_F	128_L	0.997	1.00
62_E	66_A	0.989	1.00
26_L	31_Y	0.988	1.00
24_W	27_R	0.985	1.00
275_V	286_V	0.982	0.99
13_G	17_Y	0.979	0.99
215_F	219_I	0.973	0.99
110_P	118_R	0.973	0.99
284_A	291_S	0.972	0.99
242_S	245_D	0.962	0.99
195_S	273_R	0.961	0.99
22_A	33_G	0.955	0.99
97_L	101_L	0.955	0.99
76_L	149_A	0.951	0.99
3_A	6_A	0.951	0.99
137_P	141_L	0.948	0.99
127_A	130_A	0.946	0.99
194_R	201_G	0.942	0.99
9_D	16_G	0.921	0.99
187_D	190_L	0.916	0.99
25_S	28_F	0.915	0.99
10_L	15_Y	0.915	0.99
206_F	264_A	0.910	0.99
160_E	164_Q	0.906	0.99
150_R	232_W	0.906	0.99
18_R	21_G	0.905	0.99
251_A	255_R	0.902	0.99
148_Q	151_A	0.900	0.99
125_L	129_L	0.899	0.99
58_A	61_E	0.898	0.99
30_L	33_G	0.895	0.99
154_R	236_D	0.892	0.99
46_R	50_R	0.891	0.99
196_S	264_A	0.888	0.99
80_L	146_V	0.888	0.99
281_A	284_A	0.887	0.99
58_A	62_E	0.884	0.99
204_G	210_G	0.881	0.99
286_V	289_L	0.880	0.99
145_L	148_Q	0.880	0.99
76_L	152_T	0.876	0.99
98_K	123_A	0.875	0.99
135_I	138_L	0.873	0.99
77_Y	233_V	0.870	0.99
217_P	220_D	0.869	0.99
207_T	261_Y	0.866	0.99
212_E	216_L	0.859	0.99
192_F	274_V	0.854	0.99
106_Q	110_P	0.852	0.99
53_L	128_L	0.851	0.99
75_A	103_R	0.849	0.99
194_R	272_L	0.847	0.98
260_D	264_A	0.845	0.98
289_L	296_P	0.844	0.98
111_G	116_Q	0.840	0.98
63_Q	104_D	0.839	0.98
81_K	229_E	0.838	0.98
43_A	46_R	0.834	0.98
196_S	201_G	0.834	0.98
184_L	192_F	0.830	0.98
213_E	217_P	0.823	0.98
63_Q	75_A	0.822	0.98
47_A	50_R	0.822	0.98
241_A	245_D	0.820	0.98
12_A	16_G	0.818	0.98
305_A	308_T	0.815	0.98
94_A	130_A	0.809	0.98
125_L	128_L	0.809	0.98
112_D	118_R	0.804	0.98
165_R	169_E	0.801	0.98
151_A	155_R	0.800	0.98
113_A	117_Q	0.799	0.98
260_D	263_A	0.796	0.98
202_V	268_F	0.796	0.98
162_V	253_L	0.792	0.98
221_E	224_K	0.790	0.98
150_R	235_G	0.783	0.97
277_F	282_D	0.781	0.97
122_L	125_L	0.778	0.97
91_H	232_W	0.776	0.97
8_R	127_A	0.776	0.97
267_A	271_D	0.776	0.97
100_W	104_D	0.775	0.97
67_L	76_L	0.774	0.97
6_A	10_L	0.772	0.97
47_A	51_L	0.771	0.97
157_P	160_E	0.768	0.97
75_A	78_E	0.759	0.97
210_G	219_I	0.759	0.97
295_S	298_L	0.755	0.97
208_R	306_R	0.755	0.97
223_A	246_P	0.744	0.97
110_P	113_A	0.743	0.97
7_L	11_P	0.737	0.96
177_D	200_E	0.737	0.96
224_K	246_P	0.736	0.96
150_R	233_V	0.736	0.96
264_A	267_A	0.733	0.96
65_R	145_L	0.731	0.96
274_V	277_F	0.731	0.96
106_Q	118_R	0.728	0.96
83_Y	146_V	0.727	0.96
15_Y	19_R	0.727	0.96
135_I	141_L	0.725	0.96
81_K	232_W	0.724	0.96
180_L	184_L	0.724	0.96
121_L	125_L	0.717	0.96
146_V	232_W	0.717	0.96
80_L	233_V	0.715	0.96
11_P	40_A	0.714	0.96
27_R	31_Y	0.713	0.96
19_R	22_A	0.712	0.96
256_L	259_A	0.711	0.96
226_L	229_E	0.710	0.96
74_E	78_E	0.710	0.96
97_L	129_L	0.710	0.96
64_L	79_A	0.710	0.96
77_Y	84_L	0.710	0.96
8_R	11_P	0.708	0.95
192_F	196_S	0.707	0.95
78_E	165_R	0.705	0.95
243_E	246_P	0.705	0.95
34_D	38_A	0.703	0.95
51_L	55_R	0.701	0.95
123_A	126_A	0.700	0.95
190_L	289_L	0.698	0.95
302_R	306_R	0.694	0.95
37_G	41_R	0.693	0.95
86_L	184_L	0.689	0.95
17_Y	21_G	0.688	0.95
268_F	271_D	0.685	0.95
147_A	154_R	0.685	0.95
180_L	272_L	0.682	0.94
180_L	188_A	0.682	0.94
108_A	111_G	0.680	0.94
288_R	292_G	0.678	0.94
2_P	6_A	0.671	0.94
170_A	210_G	0.669	0.94
240_A	243_E	0.669	0.94
175_L	214_V	0.665	0.94
38_A	41_R	0.663	0.94
10_L	26_L	0.662	0.94
247_A	250_A	0.661	0.93
304_V	308_T	0.658	0.93
101_L	104_D	0.654	0.93
169_E	218_A	0.653	0.93
49_R	131_L	0.652	0.93
44_Y	295_S	0.651	0.93
78_E	96_F	0.650	0.93
74_E	164_Q	0.644	0.93
80_L	149_A	0.643	0.93
183_A	303_A	0.643	0.93
110_P	115_A	0.641	0.92
120_A	123_A	0.639	0.92
185_G	190_L	0.637	0.92
219_I	222_A	0.636	0.92
166_L	215_F	0.634	0.92
83_Y	280_L	0.630	0.92
12_A	17_Y	0.630	0.92
274_V	283_A	0.629	0.92
3_A	7_L	0.628	0.92
89_P	126_A	0.625	0.91
27_R	30_L	0.624	0.91
6_A	9_D	0.623	0.91
261_Y	307_N	0.623	0.91
29_G	33_G	0.622	0.91
288_R	291_S	0.622	0.91
192_F	304_V	0.618	0.91
112_D	117_Q	0.617	0.91
110_P	114_G	0.616	0.91
185_G	194_R	0.615	0.91
23_P	27_R	0.612	0.91
166_L	254_R	0.610	0.90
191_V	289_L	0.610	0.90
196_S	267_A	0.609	0.90
292_G	295_S	0.606	0.90
17_Y	23_P	0.605	0.90
55_R	58_A	0.603	0.90
78_E	103_R	0.601	0.90
47_A	72_D	0.601	0.90
48_L	124_H	0.598	0.90
146_V	233_V	0.596	0.89
73_P	152_T	0.595	0.89
166_L	214_V	0.593	0.89
251_A	254_R	0.588	0.89
249_L	252_D	0.587	0.89
81_K	223_A	0.586	0.89
87_G	91_H	0.585	0.89
220_D	238_A	0.585	0.89
20_D	23_P	0.584	0.88
2_P	5_D	0.583	0.88
223_A	253_L	0.583	0.88
124_H	129_L	0.581	0.88
76_L	79_A	0.581	0.88
52_L	125_L	0.580	0.88
291_S	295_S	0.579	0.88
167_K	256_L	0.578	0.88
215_F	254_R	0.577	0.88
250_A	254_R	0.577	0.88
109_L	114_G	0.576	0.88
216_L	254_R	0.574	0.88
275_V	280_L	0.574	0.88
113_A	118_R	0.574	0.88
297_L	300_L	0.573	0.88
169_E	225_Q	0.572	0.87
158_L	226_L	0.572	0.87
15_Y	37_G	0.572	0.87
227_A	230_D	0.571	0.87
246_P	250_A	0.570	0.87
18_R	22_A	0.570	0.87
52_L	104_D	0.569	0.87
280_L	283_A	0.569	0.87
64_L	145_L	0.568	0.87
114_G	243_E	0.564	0.87
285_D	289_L	0.564	0.87
8_R	123_A	0.563	0.87
154_R	237_S	0.563	0.87
209_D	212_E	0.562	0.87
152_T	211_Y	0.561	0.86
78_E	164_Q	0.559	0.86
178_F	207_T	0.558	0.86
48_L	54_P	0.557	0.86
43_A	47_A	0.556	0.86
258_F	261_Y	0.556	0.86
46_R	49_R	0.553	0.86
167_K	170_A	0.552	0.86
191_V	275_V	0.551	0.85
162_V	165_R	0.549	0.85
96_F	101_L	0.548	0.85
95_A	99_A	0.547	0.85
105_W	122_L	0.545	0.85
261_Y	268_F	0.545	0.85
66_A	69_A	0.543	0.85
207_T	210_G	0.543	0.85
92_L	129_L	0.542	0.85
211_Y	254_R	0.541	0.84
283_A	307_N	0.540	0.84
149_A	152_T	0.540	0.84
241_A	244_A	0.539	0.84
298_L	301_L	0.538	0.84
302_R	305_A	0.538	0.84
22_A	25_S	0.538	0.84
252_D	256_L	0.537	0.84
286_V	308_T	0.536	0.84
197_P	200_E	0.536	0.84
4_L	52_L	0.535	0.84
81_K	168_A	0.535	0.84
279_S	283_A	0.534	0.84
5_D	12_A	0.534	0.84
62_E	65_R	0.533	0.84
82_A	101_L	0.531	0.83
156_L	161_R	0.529	0.83
162_V	226_L	0.529	0.83
116_Q	119_E	0.529	0.83
56_L	125_L	0.527	0.83
239_A	243_E	0.526	0.83
128_L	131_L	0.525	0.83
203_P	206_F	0.525	0.83
83_Y	257_Y	0.525	0.83
185_G	196_S	0.524	0.83
23_P	31_Y	0.524	0.83
287_L	291_S	0.523	0.82
166_L	218_A	0.523	0.82
264_A	268_F	0.522	0.82
188_A	198_L	0.522	0.82
80_L	150_R	0.522	0.82
274_V	290_L	0.521	0.82
186_P	193_T	0.521	0.82
105_W	129_L	0.518	0.82
123_A	127_A	0.518	0.82
209_D	306_R	0.518	0.82
15_Y	128_L	0.518	0.82
109_L	116_Q	0.517	0.82
109_L	118_R	0.517	0.82
181_A	188_A	0.517	0.82
153_L	286_V	0.517	0.82
59_R	63_Q	0.517	0.82
60_L	256_L	0.515	0.81
161_R	226_L	0.514	0.81
159_A	253_L	0.513	0.81
237_S	240_A	0.513	0.81
198_L	201_G	0.513	0.81
214_V	218_A	0.513	0.81
105_W	232_W	0.511	0.81
249_L	300_L	0.510	0.81
205_L	215_F	0.510	0.81
66_A	285_D	0.508	0.81
150_R	234_L	0.508	0.81
298_L	303_A	0.507	0.80
17_Y	22_A	0.507	0.80
135_I	207_T	0.507	0.80
75_A	79_A	0.506	0.80
148_Q	152_T	0.506	0.80
87_G	146_V	0.505	0.80
161_R	210_G	0.505	0.80
57_A	87_G	0.504	0.80
147_A	150_R	0.504	0.80
53_L	59_R	0.502	0.80
272_L	304_V	0.502	0.80
76_L	104_D	0.501	0.80
97_L	295_S	0.500	0.80

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
1qrjA	1	0.4984	3.8	0.964	Contact Map
2qkoA	2	0.3625	3.4	0.964	Contact Map
1oefA	1	0.0777	3	0.966	Contact Map
4rswA	2	0.2233	2.8	0.966	Contact Map
3r84A	2	0.1618	2.6	0.967	Contact Map
1jwyB	1	0.2071	2.2	0.968	Contact Map
4rxiA	1	0.2816	2	0.969	Contact Map
3pmkN	1	0.0809	1.9	0.969	Contact Map
1x60A	1	0.2557	1.8	0.969	Contact Map
2iaiA	2	0.356	1.8	0.969	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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