PTFD - BACSU - GREMLIN Contacts

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PTFD - Fructose permease IID component

UniProt:	P26382	Sequences: MEKEKRLTKKEIFSMFIRSNFLLGSFNFERVQAMGYCYVMIPAIKKLYGPGAKRNEALQRHLEWFNTHPWLTAPIFGVTAAMEEEMANNKGIDGKAISGMKIGLMGPIAGVGDPIFWGTIRPVLAALGASLALGGNIAGPLLFFFLLNAIRLSTKYYGLKYGYVKGMEILQDLAGNRIQKLTEGASILGLFVMGALVSKWTTINIPIVVSRIKDESGKVDVQTVQNVLDSIMPGALPLGLTLLVAWMLRKGVNPLLIICGIFVIGILGYWAGFLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	275 (263)
Sequences:	1325 (825)
Seq/√Len:	50.9

ECOLI - PTND PTPD
BACSU - PTFD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_T	109_A	5.877	1.00
44_I	54_R	4.441	1.00
253_N	256_L	4.176	1.00
11_E	46_K	3.879	1.00
8_T	11_E	3.347	1.00
43_A	80_A	3.234	1.00
259_C	263_V	3.217	1.00
50_P	53_K	3.217	1.00
243_L	246_W	3.169	1.00
223_T	226_N	3.164	1.00
56_E	94_G	2.982	1.00
226_N	229_D	2.958	1.00
239_G	243_L	2.885	1.00
7_L	80_A	2.826	1.00
268_G	274_L	2.787	1.00
264_I	268_G	2.620	1.00
128_G	139_G	2.619	1.00
36_Y	79_T	2.534	1.00
244_V	261_I	2.472	1.00
7_L	43_A	2.471	1.00
9_K	160_K	2.437	1.00
45_K	54_R	2.376	1.00
222_Q	225_Q	2.304	1.00
156_Y	160_K	2.280	1.00
51_G	55_N	2.221	1.00
75_I	109_A	2.167	1.00
225_Q	229_D	2.129	1.00
18_R	38_Y	2.119	1.00
205_I	224_V	2.114	1.00
252_V	260_G	2.028	1.00
12_I	159_L	1.884	0.99
37_C	58_L	1.883	0.99
84_E	163_Y	1.873	0.99
65_F	75_I	1.872	0.99
13_F	160_K	1.862	0.99
232_M	235_A	1.848	0.99
8_T	46_K	1.813	0.99
240_L	261_I	1.783	0.99
61_H	83_E	1.764	0.99
43_A	47_L	1.748	0.99
40_M	44_I	1.743	0.99
161_Y	164_V	1.732	0.99
86_M	94_G	1.724	0.99
125_A	143_F	1.722	0.99
53_K	56_E	1.698	0.99
7_L	11_E	1.694	0.99
267_L	271_A	1.684	0.98
67_T	75_I	1.658	0.98
23_L	26_F	1.638	0.98
203_I	274_L	1.618	0.98
205_I	236_L	1.596	0.98
82_M	96_A	1.592	0.98
237_P	241_T	1.558	0.97
252_V	256_L	1.511	0.97
65_F	72_T	1.510	0.97
267_L	270_W	1.495	0.97
61_H	101_K	1.484	0.97
25_S	34_M	1.466	0.96
75_I	108_I	1.411	0.95
49_G	52_A	1.410	0.95
137_I	140_P	1.405	0.95
39_V	76_F	1.401	0.95
86_M	97_I	1.397	0.95
19_S	72_T	1.387	0.95
63_E	98_S	1.383	0.95
5_K	88_N	1.373	0.95
7_L	12_I	1.367	0.94
263_V	267_L	1.349	0.94
15_M	43_A	1.344	0.94
206_P	274_L	1.298	0.93
54_R	58_L	1.289	0.93
139_G	142_L	1.287	0.92
89_N	92_I	1.285	0.92
12_I	160_K	1.283	0.92
59_Q	62_L	1.278	0.92
142_L	146_L	1.276	0.92
160_K	164_V	1.268	0.92
48_Y	57_A	1.268	0.92
244_V	257_I	1.255	0.92
235_A	239_G	1.247	0.91
6_R	88_N	1.243	0.91
98_S	102_I	1.235	0.91
22_L	32_Q	1.217	0.90
197_V	241_T	1.216	0.90
257_I	261_I	1.203	0.90
129_A	133_L	1.199	0.90
44_I	57_A	1.193	0.89
32_Q	109_A	1.180	0.89
203_I	236_L	1.169	0.88
247_M	252_V	1.165	0.88
73_A	159_L	1.165	0.88
255_L	259_C	1.156	0.88
165_K	172_D	1.153	0.88
124_L	146_L	1.151	0.88
247_M	260_G	1.141	0.87
41_I	58_L	1.133	0.87
65_F	76_F	1.126	0.86
86_M	89_N	1.124	0.86
16_F	156_Y	1.122	0.86
27_N	30_R	1.114	0.86
35_G	163_Y	1.109	0.85
55_N	59_Q	1.108	0.85
256_L	260_G	1.107	0.85
141_L	145_F	1.106	0.85
22_L	72_T	1.097	0.85
238_L	242_L	1.095	0.85
140_P	143_F	1.090	0.84
26_F	33_A	1.084	0.84
271_A	274_L	1.084	0.84
52_A	55_N	1.078	0.84
37_C	41_I	1.077	0.84
30_R	33_A	1.070	0.83
268_G	273_F	1.062	0.83
86_M	92_I	1.058	0.83
9_K	13_F	1.042	0.82
10_K	14_S	1.038	0.81
121_R	143_F	1.025	0.81
226_N	271_A	1.011	0.80
69_P	192_V	1.008	0.79
71_L	108_I	1.001	0.79
36_Y	61_H	1.001	0.79
31_V	116_F	0.999	0.79
80_A	159_L	0.996	0.79
60_R	101_K	0.995	0.79
32_Q	67_T	0.991	0.78
153_S	157_Y	0.989	0.78
139_G	144_F	0.983	0.78
15_M	159_L	0.983	0.78
165_K	168_E	0.982	0.78
51_G	54_R	0.981	0.78
226_N	230_S	0.979	0.77
203_I	240_L	0.976	0.77
57_A	60_R	0.970	0.77
268_G	271_A	0.965	0.76
13_F	156_Y	0.965	0.76
16_F	155_K	0.964	0.76
154_T	158_G	0.963	0.76
266_I	270_W	0.960	0.76
44_I	47_L	0.956	0.76
47_L	88_N	0.952	0.75
85_E	89_N	0.946	0.75
11_E	14_S	0.941	0.75
208_V	218_K	0.941	0.75
203_I	237_P	0.934	0.74
131_L	134_G	0.927	0.74
240_L	262_F	0.920	0.73
36_Y	40_M	0.919	0.73
111_V	152_L	0.919	0.73
150_I	196_L	0.914	0.72
37_C	40_M	0.913	0.72
128_G	146_L	0.897	0.71
30_R	62_L	0.895	0.71
23_L	31_V	0.891	0.71
14_S	46_K	0.890	0.70
37_C	45_K	0.890	0.70
61_H	79_T	0.889	0.70
224_V	230_S	0.885	0.70
240_L	264_I	0.882	0.70
221_V	225_Q	0.881	0.70
144_F	148_N	0.880	0.70
204_N	268_G	0.878	0.69
131_L	184_G	0.873	0.69
122_P	196_L	0.868	0.68
49_G	53_K	0.865	0.68
20_N	152_L	0.864	0.68
145_F	149_A	0.855	0.67
96_A	99_G	0.853	0.67
14_S	18_R	0.851	0.67
205_I	274_L	0.846	0.66
249_R	271_A	0.844	0.66
222_Q	226_N	0.840	0.66
27_N	241_T	0.835	0.65
122_P	150_I	0.835	0.65
65_F	105_M	0.834	0.65
261_I	265_G	0.826	0.65
150_I	153_S	0.824	0.64
240_L	244_V	0.822	0.64
125_A	129_A	0.822	0.64
15_M	80_A	0.818	0.64
19_S	125_A	0.815	0.64
168_E	171_Q	0.815	0.64
11_E	84_E	0.808	0.63
260_G	264_I	0.806	0.63
40_M	47_L	0.804	0.63
138_A	141_L	0.803	0.62
207_I	236_L	0.802	0.62
52_A	149_A	0.794	0.62
202_T	234_G	0.793	0.61
53_K	235_A	0.788	0.61
6_R	49_G	0.787	0.61
221_V	224_V	0.786	0.61
15_M	38_Y	0.785	0.61
124_L	150_I	0.773	0.59
74_P	158_G	0.772	0.59
13_F	17_I	0.770	0.59
225_Q	228_L	0.762	0.58
205_I	223_T	0.760	0.58
146_L	228_L	0.755	0.58
260_G	263_V	0.752	0.57
27_N	69_P	0.744	0.57
74_P	170_L	0.739	0.56
103_G	154_T	0.738	0.56
245_A	249_R	0.738	0.56
96_A	100_M	0.733	0.55
22_L	35_G	0.730	0.55
68_H	116_F	0.728	0.55
35_G	42_P	0.725	0.55
7_L	47_L	0.724	0.54
20_N	73_A	0.722	0.54
123_V	127_L	0.721	0.54
48_Y	109_A	0.720	0.54
265_G	269_Y	0.719	0.54
47_L	84_E	0.713	0.53
124_L	145_F	0.713	0.53
108_I	153_S	0.710	0.53
47_L	75_I	0.703	0.52
115_I	168_E	0.700	0.52
34_M	62_L	0.700	0.52
246_W	249_R	0.696	0.52
10_K	17_I	0.689	0.51
184_G	188_L	0.687	0.51
124_L	141_L	0.684	0.50
19_S	118_G	0.683	0.50
243_L	260_G	0.683	0.50
45_K	58_L	0.682	0.50
227_V	230_S	0.677	0.50
196_L	200_W	0.674	0.49
40_M	98_S	0.673	0.49
237_P	242_L	0.672	0.49
224_V	227_V	0.671	0.49
5_K	49_G	0.669	0.49
62_L	144_F	0.664	0.48
207_I	224_V	0.663	0.48
203_I	206_P	0.663	0.48
260_G	268_G	0.662	0.48
93_D	182_T	0.661	0.48
263_V	272_G	0.661	0.48
36_Y	101_K	0.660	0.48
177_R	180_K	0.658	0.48
89_N	94_G	0.654	0.47
123_V	139_G	0.653	0.47
33_A	62_L	0.651	0.47
47_L	87_A	0.650	0.47
26_F	188_L	0.649	0.47
82_M	161_Y	0.648	0.47
204_N	269_Y	0.646	0.46
46_K	163_Y	0.644	0.46
41_I	54_R	0.643	0.46
242_L	245_A	0.643	0.46
86_M	93_D	0.642	0.46
95_K	179_Q	0.642	0.46
25_S	228_L	0.641	0.46
205_I	228_L	0.639	0.46
19_S	155_K	0.638	0.46
35_G	125_A	0.635	0.45
63_E	95_K	0.635	0.45
82_M	234_G	0.631	0.45
110_G	118_G	0.629	0.45
180_K	187_I	0.629	0.45
208_V	220_D	0.629	0.45
201_T	237_P	0.627	0.45
210_S	216_S	0.627	0.45
100_M	188_L	0.626	0.44
120_I	150_I	0.624	0.44
60_R	87_A	0.621	0.44
202_T	219_V	0.617	0.43
83_E	194_G	0.616	0.43
192_V	234_G	0.614	0.43
25_S	38_Y	0.614	0.43
55_N	99_G	0.613	0.43
73_A	158_G	0.612	0.43
111_V	114_P	0.610	0.43
158_G	241_T	0.610	0.43
50_P	55_N	0.607	0.42
6_R	84_E	0.603	0.42
168_E	264_I	0.602	0.42
123_V	194_G	0.601	0.42
87_A	118_G	0.601	0.42
207_I	273_F	0.600	0.42
55_N	58_L	0.600	0.42
79_T	83_E	0.599	0.42
146_L	262_F	0.598	0.42
64_W	97_I	0.598	0.42
209_V	227_V	0.591	0.41
133_L	208_V	0.590	0.41
248_L	251_G	0.590	0.41
99_G	102_I	0.589	0.41
178_I	198_S	0.588	0.41
181_L	188_L	0.588	0.41
59_Q	138_A	0.587	0.40
184_G	195_A	0.585	0.40
110_G	162_G	0.583	0.40
87_A	119_T	0.582	0.40
77_G	194_G	0.582	0.40
17_I	20_N	0.582	0.40
114_P	151_R	0.581	0.40
80_A	84_E	0.581	0.40
216_S	227_V	0.580	0.40
11_E	43_A	0.580	0.40
199_K	234_G	0.579	0.40
185_A	254_P	0.577	0.39
242_L	257_I	0.577	0.39
136_N	139_G	0.577	0.39
142_L	145_F	0.574	0.39
247_M	251_G	0.573	0.39
176_N	179_Q	0.573	0.39
103_G	109_A	0.572	0.39
118_G	121_R	0.572	0.39
25_S	109_A	0.571	0.39
201_T	241_T	0.569	0.39
64_W	178_I	0.569	0.39
27_N	33_A	0.569	0.39
48_Y	104_L	0.568	0.39
5_K	47_L	0.568	0.39
56_E	95_K	0.567	0.38
132_A	196_L	0.567	0.38
42_P	271_A	0.566	0.38
110_G	126_A	0.565	0.38
49_G	54_R	0.565	0.38
95_K	249_R	0.565	0.38
31_V	68_H	0.564	0.38
231_I	251_G	0.563	0.38
33_A	228_L	0.562	0.38
68_H	72_T	0.562	0.38
68_H	122_P	0.562	0.38
114_P	200_W	0.561	0.38
149_A	153_S	0.558	0.38
12_I	39_V	0.556	0.37
70_W	73_A	0.555	0.37
210_S	220_D	0.552	0.37
225_Q	230_S	0.552	0.37
100_M	170_L	0.552	0.37
23_L	69_P	0.552	0.37
203_I	264_I	0.551	0.37
6_R	53_K	0.549	0.37
99_G	103_G	0.547	0.37
28_F	33_A	0.546	0.36
16_F	20_N	0.546	0.36
23_L	197_V	0.545	0.36
66_N	189_G	0.544	0.36
8_T	84_E	0.542	0.36
23_L	28_F	0.542	0.36
7_L	84_E	0.541	0.36
141_L	239_G	0.541	0.36
156_Y	159_L	0.540	0.36
130_S	143_F	0.538	0.36
118_G	241_T	0.538	0.36
126_A	151_R	0.537	0.36
270_W	273_F	0.536	0.35
138_A	142_L	0.536	0.35
254_P	258_I	0.536	0.35
252_V	255_L	0.536	0.35
157_Y	161_Y	0.536	0.35
208_V	223_T	0.535	0.35
192_V	233_P	0.535	0.35
186_S	190_L	0.535	0.35
236_L	272_G	0.534	0.35
236_L	239_G	0.533	0.35
152_L	191_F	0.531	0.35
259_C	273_F	0.530	0.35
149_A	273_F	0.530	0.35
5_K	12_I	0.528	0.35
103_G	202_T	0.527	0.35
87_A	230_S	0.526	0.35
141_L	270_W	0.526	0.35
217_G	221_V	0.526	0.35
50_P	54_R	0.525	0.34
97_I	118_G	0.523	0.34
180_K	265_G	0.522	0.34
11_E	15_M	0.522	0.34
85_E	167_M	0.522	0.34
141_L	161_Y	0.521	0.34
78_V	230_S	0.521	0.34
132_A	136_N	0.517	0.34
114_P	230_S	0.515	0.34
26_F	254_P	0.515	0.34
61_H	103_G	0.514	0.33
56_E	161_Y	0.514	0.33
65_F	108_I	0.514	0.33
9_K	181_L	0.513	0.33
77_G	83_E	0.511	0.33
15_M	18_R	0.510	0.33
97_I	126_A	0.507	0.33
88_N	229_D	0.507	0.33
123_V	235_A	0.505	0.33
25_S	29_E	0.504	0.33
19_S	25_S	0.504	0.33
75_I	79_T	0.504	0.33
176_N	185_A	0.503	0.32
226_N	267_L	0.502	0.32
5_K	251_G	0.501	0.32
103_G	265_G	0.500	0.32
64_W	110_G	0.500	0.32
127_L	191_F	0.500	0.32

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
3pf6A	2	0.1964	14.7	0.973	Contact Map
4afiA	2	0.2473	14.6	0.973	Contact Map
1oahA	2	0.32	12.2	0.974	Contact Map
2xq0A	1	0.2873	5.6	0.978	Contact Map
2h3oA	1	0.16	5.3	0.978	Contact Map
4hygA	3	0.3127	5.1	0.978	Contact Map
2vwaA	1	0.2036	4.2	0.979	Contact Map
3b60A	2	0.6145	4	0.979	Contact Map
3k9aA	3	0.08	3.9	0.979	Contact Map
2rr7A	1	0.1964	3.8	0.979	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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