PTPD - ECOLI - GREMLIN Contacts

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PTPD - N-acetylgalactosamine permease IID component

UniProt:	P42911	Sequences: MGSEISKKDITRLGFRSSLLQASFNYERMQAGGFTWAMLPILKKIYKDDKPGLSAAMKDNLEFINTHPNLVGFLMGLLISMEEKGENRDTIKGLKVALFGPIAGIGDAIFWFTLLPIMAGICSSFASQGNLLGPILFFAVYLLIFFLRVGWTHVGYSVGVKAIDKVRENSQMIARSATILGITVIGGLIASYVHINVVTSFAIDNTHSVALQQDFFDKVFPNILPMAYTLLMYYFLRVKKAHPVLLIGVTFVLSIVCSAFGIL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12771
Length:	263 (255)
Sequences:	1316 (829)
Seq/√Len:	51.9

ECOLI - PTPD PTND
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
66_T	103_A	5.704	1.00
42_L	53_L	4.351	1.00
242_H	245_L	4.151	1.00
9_D	44_K	3.744	1.00
48_D	52_G	3.304	1.00
6_S	9_D	3.275	1.00
50_K	54_S	3.249	1.00
248_G	252_V	3.211	1.00
41_I	79_I	3.064	1.00
231_L	234_Y	3.045	1.00
227_A	231_L	2.848	1.00
214_D	217_D	2.805	1.00
213_Q	217_D	2.768	1.00
5_I	79_I	2.760	1.00
197_V	212_Q	2.757	1.00
211_L	214_D	2.741	1.00
253_L	257_C	2.593	1.00
5_I	41_I	2.559	1.00
122_C	133_G	2.543	1.00
34_F	78_L	2.443	1.00
232_M	250_T	2.438	1.00
43_K	53_L	2.389	1.00
7_K	153_H	2.278	1.00
149_V	153_H	2.260	1.00
74_L	103_A	2.093	1.00
16_R	36_W	2.084	1.00
64_I	74_L	1.928	0.99
241_A	249_V	1.885	0.99
10_I	152_T	1.867	0.99
83_E	156_Y	1.861	0.99
21_Q	24_F	1.810	0.99
6_S	44_K	1.807	0.99
11_T	153_H	1.799	0.99
35_T	57_M	1.789	0.99
60_N	82_E	1.768	0.99
228_Y	250_T	1.755	0.99
256_V	260_F	1.745	0.99
154_V	157_S	1.742	0.99
220_F	223_I	1.738	0.99
41_I	45_I	1.730	0.99
38_M	42_L	1.720	0.99
119_A	137_F	1.717	0.99
66_T	74_L	1.659	0.98
47_K	52_G	1.640	0.98
225_P	229_T	1.589	0.98
17_S	71_V	1.568	0.98
197_V	224_L	1.565	0.98
81_M	90_T	1.511	0.97
241_A	245_L	1.501	0.97
200_S	209_V	1.483	0.97
85_G	91_I	1.446	0.96
131_L	134_P	1.434	0.96
23_S	32_G	1.432	0.96
60_N	95_K	1.429	0.96
52_G	55_A	1.394	0.95
37_A	75_M	1.391	0.95
256_V	259_A	1.382	0.95
64_I	71_V	1.379	0.95
62_E	92_K	1.377	0.95
133_G	136_L	1.366	0.95
74_L	102_I	1.362	0.95
199_T	212_Q	1.355	0.95
50_K	53_L	1.334	0.94
5_I	9_D	1.317	0.94
232_M	246_L	1.294	0.93
48_D	51_P	1.287	0.93
202_A	209_V	1.285	0.93
118_M	140_V	1.283	0.93
233_Y	237_R	1.277	0.93
252_V	256_V	1.268	0.92
136_L	140_V	1.267	0.92
58_K	61_L	1.257	0.92
53_L	57_M	1.253	0.92
135_I	139_A	1.248	0.92
10_I	153_H	1.246	0.92
235_F	241_A	1.238	0.91
153_H	157_S	1.236	0.91
46_Y	56_A	1.232	0.91
30_Q	103_A	1.227	0.91
51_P	55_A	1.226	0.91
13_L	41_I	1.212	0.90
20_L	30_Q	1.210	0.90
123_S	127_S	1.209	0.90
42_L	56_A	1.207	0.90
5_I	10_I	1.207	0.90
92_K	96_V	1.205	0.90
39_L	57_M	1.187	0.90
139_A	143_L	1.179	0.89
14_G	149_V	1.170	0.89
223_I	227_A	1.161	0.88
189_I	229_T	1.160	0.88
235_F	249_V	1.156	0.88
246_L	250_T	1.156	0.88
244_V	248_G	1.144	0.88
72_G	152_T	1.140	0.88
158_V	165_K	1.128	0.87
47_K	50_K	1.118	0.87
35_T	39_L	1.114	0.86
54_S	58_K	1.106	0.86
134_P	137_F	1.101	0.86
25_N	28_R	1.097	0.85
8_K	12_R	1.095	0.85
24_F	31_A	1.094	0.85
226_M	230_L	1.081	0.85
245_L	249_V	1.080	0.85
195_I	224_L	1.078	0.84
30_Q	66_T	1.076	0.84
64_I	75_M	1.065	0.84
33_G	156_Y	1.063	0.84
56_A	59_D	1.058	0.83
158_V	161_K	1.050	0.83
28_R	31_A	1.049	0.83
13_L	152_T	1.030	0.82
59_D	95_K	1.030	0.82
68_P	184_V	1.029	0.82
7_K	11_T	1.026	0.81
257_C	262_I	1.024	0.81
38_M	45_I	1.022	0.81
115_L	137_F	1.005	0.80
257_C	260_F	1.005	0.80
214_D	260_F	1.004	0.80
228_Y	251_F	1.003	0.80
146_F	150_G	1.000	0.80
21_Q	29_M	0.998	0.80
116_P	188_L	0.988	0.79
105_I	145_F	0.988	0.79
147_L	151_W	0.984	0.79
43_K	50_K	0.974	0.78
34_F	38_M	0.973	0.78
52_G	56_A	0.973	0.78
14_G	148_R	0.963	0.77
11_T	149_V	0.962	0.77
42_L	45_I	0.959	0.77
136_L	139_A	0.956	0.77
255_I	259_A	0.951	0.76
51_P	54_S	0.951	0.76
196_N	257_C	0.950	0.76
29_M	110_F	0.941	0.75
70_L	102_I	0.936	0.75
79_I	152_T	0.933	0.75
12_R	44_K	0.931	0.75
34_F	60_N	0.923	0.74
214_D	218_K	0.921	0.74
9_D	12_R	0.920	0.74
85_G	88_R	0.918	0.74
195_I	228_Y	0.916	0.73
118_M	144_I	0.915	0.73
133_G	138_F	0.914	0.73
45_I	87_N	0.906	0.73
195_I	198_V	0.906	0.73
60_N	78_L	0.905	0.72
125_F	128_Q	0.902	0.72
167_R	170_S	0.901	0.72
64_I	99_F	0.893	0.71
213_Q	216_F	0.876	0.70
28_R	61_L	0.873	0.70
250_T	254_S	0.870	0.69
45_I	52_G	0.868	0.69
228_Y	232_M	0.867	0.69
125_F	176_S	0.863	0.69
20_L	71_V	0.859	0.68
132_L	135_I	0.859	0.68
35_T	38_M	0.855	0.68
13_L	79_I	0.840	0.67
194_H	222_N	0.839	0.67
195_I	225_P	0.835	0.66
11_T	15_F	0.832	0.66
4_E	47_K	0.831	0.66
161_K	164_D	0.828	0.66
228_Y	253_L	0.822	0.65
116_P	144_I	0.820	0.65
18_S	145_F	0.819	0.65
12_R	16_R	0.812	0.64
205_N	209_V	0.809	0.64
52_G	60_N	0.808	0.64
210_A	215_F	0.807	0.64
90_T	93_G	0.804	0.63
9_D	83_E	0.803	0.63
117_I	133_G	0.802	0.63
73_F	151_W	0.801	0.63
51_P	205_N	0.800	0.63
13_L	36_W	0.797	0.63
35_T	43_K	0.794	0.62
46_Y	103_A	0.784	0.61
102_I	146_F	0.784	0.61
249_V	253_L	0.784	0.61
25_N	229_T	0.783	0.61
119_A	123_S	0.779	0.61
17_S	20_L	0.775	0.60
114_L	144_I	0.774	0.60
4_E	87_N	0.767	0.60
38_M	92_K	0.765	0.59
43_K	57_M	0.763	0.59
84_K	88_R	0.763	0.59
200_S	205_N	0.762	0.59
67_H	110_F	0.762	0.59
254_S	258_S	0.762	0.59
18_S	72_G	0.761	0.59
73_F	163_I	0.759	0.59
118_M	139_A	0.755	0.58
176_S	180_L	0.751	0.58
45_I	74_L	0.746	0.58
61_L	138_F	0.743	0.57
90_T	94_L	0.743	0.57
249_V	252_V	0.743	0.57
144_I	188_L	0.742	0.57
44_K	156_Y	0.740	0.57
225_P	230_L	0.738	0.57
17_S	112_F	0.737	0.57
109_I	161_K	0.733	0.56
45_I	83_E	0.732	0.56
230_L	233_Y	0.731	0.56
188_L	192_Y	0.729	0.56
57_M	239_K	0.726	0.55
10_I	37_A	0.723	0.55
17_S	119_A	0.720	0.55
215_F	218_K	0.719	0.55
138_F	142_L	0.716	0.54
117_I	121_I	0.714	0.54
248_G	262_I	0.713	0.54
162_A	167_R	0.713	0.54
15_F	143_L	0.710	0.54
52_G	223_I	0.709	0.54
45_I	86_E	0.706	0.53
59_D	86_E	0.704	0.53
21_Q	30_Q	0.704	0.53
25_N	68_P	0.704	0.53
86_E	112_F	0.697	0.52
97_A	147_L	0.697	0.52
33_G	40_P	0.696	0.52
32_G	61_L	0.695	0.52
23_S	216_F	0.694	0.52
34_F	95_K	0.686	0.51
231_L	249_V	0.678	0.50
199_T	224_L	0.678	0.50
62_E	89_D	0.677	0.50
219_V	240_K	0.674	0.50
81_M	154_V	0.667	0.49
252_V	261_G	0.667	0.49
104_G	112_F	0.666	0.49
28_R	50_K	0.665	0.49
118_M	135_I	0.662	0.49
54_S	93_G	0.661	0.49
249_V	257_C	0.659	0.49
199_T	262_I	0.658	0.48
173_I	180_L	0.658	0.48
200_S	211_L	0.655	0.48
46_Y	98_L	0.655	0.48
196_N	258_S	0.652	0.48
164_D	168_E	0.651	0.48
31_A	61_L	0.648	0.47
112_F	115_L	0.645	0.47
236_L	240_K	0.642	0.47
17_S	148_R	0.642	0.47
130_N	133_G	0.640	0.47
50_K	63_F	0.640	0.47
105_I	108_A	0.639	0.46
47_K	53_L	0.638	0.46
127_S	200_S	0.637	0.46
121_I	166_V	0.632	0.46
89_D	171_Q	0.632	0.46
151_W	229_T	0.629	0.45
78_L	82_E	0.628	0.45
82_E	186_G	0.628	0.45
4_E	83_E	0.627	0.45
81_M	222_N	0.625	0.45
94_L	163_I	0.624	0.45
117_I	186_G	0.619	0.44
178_T	182_I	0.619	0.44
58_K	132_L	0.617	0.44
197_V	216_F	0.616	0.44
94_L	180_L	0.615	0.44
243_P	247_I	0.615	0.44
259_A	262_I	0.614	0.44
26_Y	31_A	0.609	0.43
195_I	253_L	0.607	0.43
126_A	188_L	0.607	0.43
76_G	186_G	0.606	0.43
8_K	15_F	0.606	0.43
132_L	217_D	0.606	0.43
193_V	225_P	0.605	0.43
79_I	83_E	0.603	0.43
93_G	96_V	0.603	0.43
33_G	119_A	0.603	0.43
81_M	168_E	0.602	0.43
104_G	120_G	0.602	0.43
104_G	155_G	0.602	0.43
21_Q	26_Y	0.602	0.43
167_R	174_A	0.600	0.42
23_S	36_W	0.599	0.42
176_S	187_G	0.599	0.42
24_F	180_L	0.598	0.42
114_L	204_D	0.598	0.42
184_V	222_N	0.594	0.42
150_G	154_V	0.593	0.42
91_I	120_G	0.592	0.42
9_D	13_L	0.589	0.41
250_T	257_C	0.589	0.41
39_L	53_L	0.589	0.41
108_A	192_Y	0.589	0.41
169_N	247_I	0.587	0.41
72_G	151_W	0.586	0.41
198_V	211_L	0.585	0.41
224_L	261_G	0.585	0.41
48_D	53_L	0.583	0.41
67_H	116_P	0.582	0.41
97_A	103_A	0.582	0.41
145_F	183_T	0.582	0.41
50_K	72_G	0.580	0.40
9_D	41_I	0.579	0.40
74_L	78_L	0.577	0.40
122_C	140_V	0.575	0.40
229_T	237_R	0.574	0.40
193_V	229_T	0.573	0.40
118_M	141_Y	0.572	0.40
230_L	246_L	0.571	0.39
40_P	260_F	0.569	0.39
29_M	67_H	0.569	0.39
65_N	181_G	0.568	0.39
25_N	31_A	0.567	0.39
63_F	104_G	0.567	0.39
7_K	173_I	0.567	0.39
55_A	89_D	0.566	0.39
203_I	210_A	0.566	0.39
108_A	218_K	0.565	0.39
211_L	262_I	0.563	0.39
191_S	222_N	0.561	0.38
91_I	112_F	0.561	0.38
130_N	190_A	0.558	0.38
84_K	160_V	0.558	0.38
110_F	147_L	0.555	0.38
177_A	243_P	0.554	0.38
135_I	259_A	0.552	0.38
83_E	87_N	0.551	0.37
235_F	240_K	0.551	0.37
86_E	113_T	0.548	0.37
55_A	154_V	0.546	0.37
201_F	215_F	0.546	0.37
5_I	45_I	0.544	0.37
24_F	210_A	0.543	0.37
70_L	150_G	0.542	0.37
161_K	253_L	0.538	0.36
81_M	117_I	0.538	0.36
172_M	254_S	0.534	0.36
76_G	82_E	0.534	0.36
143_L	252_V	0.532	0.36
214_D	256_V	0.532	0.36
15_F	18_S	0.532	0.36
124_S	137_F	0.530	0.35
60_N	97_A	0.530	0.35
120_G	203_I	0.528	0.35
23_S	103_A	0.527	0.35
67_H	103_A	0.527	0.35
122_C	132_L	0.526	0.35
27_E	61_L	0.525	0.35
135_I	154_V	0.525	0.35
241_A	244_V	0.524	0.35
126_A	130_N	0.522	0.35
180_L	188_L	0.519	0.34
54_S	57_M	0.517	0.34
211_L	217_D	0.517	0.34
236_L	243_P	0.516	0.34
97_A	194_H	0.516	0.34
71_V	185_I	0.515	0.34
224_L	227_A	0.515	0.34
184_V	214_D	0.515	0.34
13_L	17_S	0.515	0.34
98_L	103_A	0.514	0.34
172_M	179_I	0.514	0.34
41_I	247_I	0.511	0.34
14_G	18_S	0.510	0.34
13_L	16_R	0.509	0.33
87_N	217_D	0.507	0.33
121_I	137_F	0.506	0.33
160_V	217_D	0.506	0.33
117_I	147_L	0.505	0.33
132_L	136_L	0.503	0.33
48_D	54_S	0.502	0.33
109_I	136_L	0.502	0.33
24_F	69_N	0.501	0.33
161_K	262_I	0.500	0.33
117_I	223_I	0.500	0.33

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
4hygA	3	0.327	16.5	0.972	Contact Map
4afiA	2	0.251	10.8	0.974	Contact Map
2jttC	1	0.1179	10.5	0.974	Contact Map
4huqS	1	0.5741	9.6	0.975	Contact Map
1oahA	2	0.327	6.7	0.976	Contact Map
1k1fA	4	0.0875	6.5	0.977	Contact Map
3owqA	1	0.2395	6.4	0.977	Contact Map
3nddA	1	0.3422	5.9	0.977	Contact Map
4r43A	1	0.327	5.6	0.977	Contact Map
3g5sA	1	0.2738	5.3	0.978	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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