PTND - ECOLI - GREMLIN Contacts

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PTND - Mannose permease IID component

UniProt:	P69805	Sequences: MVDTTQTTTEKKLTQSDIRGVFLRSNLFQGSWNFERMQALGFCFSMVPAIRRLYPENNEARKQAIRRHLEFFNTQPFVAAPILGVTLALEEQRANGAEIDDGAINGIKVGLMGPLAGVGDPIFWGTVRPVFAALGAGIAMSGSLLGPLLFFILFNLVRLATRYYGVAYGYSKGIDIVKDMGGGFLQKLTEGASILGLFVMGALVNKWTHVNIPLVVSRITDQTGKEHVTTVQTILDQLMPGLVPLLLTFACMWLLRKKVNPLWIIVGFFVIGIAGYACGLLGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10569
Length:	283 (264)
Sequences:	1340 (835)
Seq/√Len:	51.4

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
74_T	116_A	5.899	1.00
50_I	61_R	4.373	1.00
260_N	263_W	4.077	1.00
17_D	52_R	3.797	1.00
14_T	17_D	3.381	1.00
58_N	62_K	3.287	1.00
56_E	60_A	3.236	1.00
266_V	270_V	3.206	1.00
49_A	87_L	3.153	1.00
250_A	253_W	3.075	1.00
233_T	236_D	2.937	1.00
246_L	250_A	2.930	1.00
63_Q	101_D	2.878	1.00
13_L	87_L	2.830	1.00
275_G	281_L	2.827	1.00
230_T	233_T	2.673	1.00
232_Q	236_D	2.647	1.00
271_I	275_G	2.630	1.00
135_G	146_G	2.548	1.00
13_L	49_A	2.512	1.00
212_I	231_V	2.449	1.00
42_F	86_T	2.440	1.00
251_C	268_F	2.395	1.00
51_R	61_R	2.332	1.00
163_Y	167_A	2.282	1.00
15_Q	167_A	2.259	1.00
24_R	44_F	2.061	1.00
82_I	116_A	2.057	1.00
259_V	267_G	1.953	1.00
18_I	166_V	1.881	0.99
72_F	82_I	1.869	0.99
43_C	65_I	1.864	0.99
13_L	17_D	1.843	0.99
19_R	167_A	1.841	0.99
68_H	90_E	1.833	0.99
91_E	170_Y	1.817	0.99
239_M	242_L	1.799	0.99
14_T	52_R	1.764	0.99
247_L	268_F	1.734	0.99
168_Y	171_S	1.725	0.99
274_A	278_C	1.724	0.99
132_A	150_F	1.716	0.99
49_A	53_L	1.691	0.99
93_R	101_D	1.684	0.99
46_M	50_I	1.663	0.98
72_F	79_A	1.648	0.98
29_Q	32_W	1.630	0.98
74_T	82_I	1.629	0.98
210_V	281_L	1.604	0.98
25_S	79_A	1.589	0.98
55_P	60_A	1.578	0.98
244_P	248_T	1.506	0.97
212_I	243_V	1.498	0.97
259_V	263_W	1.491	0.97
89_L	103_A	1.489	0.97
68_H	108_K	1.486	0.97
31_S	40_L	1.449	0.96
82_I	115_L	1.443	0.96
270_V	274_A	1.434	0.96
45_S	83_L	1.421	0.96
274_A	277_A	1.394	0.95
93_R	104_I	1.370	0.95
56_E	59_E	1.369	0.95
144_L	147_P	1.363	0.95
70_E	105_N	1.361	0.95
60_A	63_Q	1.339	0.94
58_N	61_R	1.337	0.94
215_V	228_V	1.332	0.94
11_K	95_N	1.313	0.93
214_L	231_V	1.311	0.93
61_R	65_I	1.292	0.93
131_F	153_L	1.292	0.93
21_V	49_A	1.283	0.93
105_N	109_V	1.283	0.93
146_G	149_L	1.282	0.93
13_L	18_I	1.263	0.92
96_G	99_I	1.259	0.92
38_Q	116_A	1.249	0.92
251_C	264_I	1.245	0.91
204_V	248_T	1.232	0.91
66_R	69_L	1.231	0.91
167_A	171_S	1.228	0.91
213_P	281_L	1.210	0.90
59_E	63_Q	1.208	0.90
278_C	281_L	1.206	0.90
18_I	167_A	1.204	0.90
50_I	64_A	1.191	0.89
210_V	243_V	1.183	0.89
136_A	140_M	1.177	0.89
80_A	166_V	1.167	0.88
263_W	267_G	1.152	0.88
72_F	83_L	1.148	0.88
16_S	20_G	1.138	0.87
254_L	267_G	1.138	0.87
262_L	266_V	1.133	0.87
149_L	153_L	1.131	0.87
215_V	225_K	1.123	0.86
217_S	228_V	1.116	0.86
41_G	170_Y	1.116	0.86
22_F	163_Y	1.114	0.86
55_P	58_N	1.112	0.86
172_K	179_D	1.109	0.86
47_V	65_I	1.106	0.86
33_N	36_R	1.099	0.85
254_L	259_V	1.097	0.85
32_W	39_A	1.096	0.85
152_I	156_L	1.083	0.84
62_K	66_R	1.081	0.84
148_L	152_I	1.075	0.84
245_L	249_F	1.074	0.84
147_P	150_F	1.073	0.84
264_I	268_F	1.071	0.84
54_Y	64_A	1.066	0.83
233_T	237_Q	1.065	0.83
242_L	246_L	1.038	0.82
275_G	278_C	1.037	0.82
28_F	38_Q	1.036	0.82
275_G	280_L	1.035	0.82
43_C	47_V	1.033	0.81
67_R	108_K	1.031	0.81
51_R	58_N	1.023	0.81
60_A	64_A	1.023	0.81
21_V	166_V	1.016	0.80
93_R	96_G	1.015	0.80
12_K	95_N	1.013	0.80
93_R	99_I	1.012	0.80
172_K	175_D	1.010	0.80
22_F	162_R	1.007	0.80
78_V	115_L	0.997	0.79
36_R	39_A	0.994	0.79
15_Q	19_R	0.987	0.78
76_P	199_V	0.986	0.78
38_Q	74_T	0.981	0.78
161_T	165_G	0.978	0.78
128_R	150_F	0.976	0.78
210_V	247_L	0.969	0.77
160_A	164_Y	0.950	0.76
19_R	163_Y	0.949	0.76
50_I	53_L	0.945	0.75
46_M	53_L	0.945	0.75
64_A	67_R	0.936	0.75
42_F	68_H	0.936	0.75
37_M	123_F	0.933	0.74
118_V	159_L	0.931	0.74
211_N	275_G	0.921	0.73
273_I	277_A	0.919	0.73
42_F	46_M	0.914	0.73
87_L	166_V	0.912	0.73
53_L	95_N	0.910	0.72
131_F	152_I	0.910	0.72
138_I	141_S	0.910	0.72
43_C	46_M	0.908	0.72
247_L	269_F	0.905	0.72
36_R	69_L	0.899	0.72
68_H	86_T	0.897	0.71
145_L	148_L	0.892	0.71
59_E	62_K	0.881	0.70
17_D	20_G	0.873	0.69
28_F	79_A	0.867	0.69
20_G	52_R	0.861	0.68
209_H	241_G	0.859	0.68
129_P	157_V	0.859	0.68
210_V	244_P	0.858	0.68
157_V	203_L	0.858	0.68
129_P	203_L	0.858	0.68
183_G	192_A	0.857	0.68
17_D	91_E	0.854	0.68
43_C	51_R	0.849	0.67
138_I	191_G	0.847	0.67
233_T	278_C	0.845	0.67
10_E	14_T	0.844	0.67
72_F	112_M	0.843	0.67
146_G	151_F	0.843	0.67
9_T	12_K	0.841	0.66
53_L	60_A	0.840	0.66
247_L	251_C	0.838	0.66
247_L	271_I	0.837	0.66
92_Q	96_G	0.837	0.66
214_L	243_V	0.828	0.65
267_G	271_I	0.826	0.65
131_F	157_V	0.825	0.65
33_N	248_T	0.824	0.65
103_A	106_G	0.824	0.65
268_F	272_G	0.820	0.64
29_Q	37_M	0.812	0.64
26_N	80_A	0.808	0.63
21_V	87_L	0.808	0.63
175_D	178_K	0.807	0.63
256_R	278_C	0.802	0.63
26_N	159_L	0.796	0.62
60_A	68_H	0.788	0.61
21_V	44_F	0.783	0.61
130_V	134_L	0.782	0.61
13_L	91_E	0.780	0.61
25_S	132_A	0.778	0.60
210_V	213_P	0.778	0.60
20_G	24_R	0.775	0.60
33_N	76_P	0.775	0.60
81_P	165_G	0.772	0.60
132_A	136_A	0.769	0.59
19_R	23_L	0.759	0.58
41_G	48_P	0.757	0.58
212_I	281_L	0.753	0.58
54_Y	116_A	0.746	0.57
131_F	148_L	0.739	0.56
81_P	177_V	0.732	0.56
53_L	91_E	0.732	0.56
149_L	152_I	0.731	0.56
135_G	153_L	0.731	0.56
151_F	155_N	0.729	0.55
252_M	256_R	0.727	0.55
127_V	157_V	0.726	0.55
103_A	107_I	0.722	0.55
215_V	230_T	0.718	0.54
60_A	242_L	0.717	0.54
115_L	160_A	0.716	0.54
272_G	276_Y	0.715	0.54
13_L	53_L	0.714	0.54
157_V	160_A	0.713	0.54
229_T	234_I	0.711	0.54
69_L	151_F	0.704	0.53
267_G	275_G	0.703	0.53
40_L	69_L	0.700	0.52
46_M	105_N	0.698	0.52
224_G	227_H	0.697	0.52
75_Q	123_F	0.695	0.52
59_E	225_K	0.694	0.52
25_S	125_G	0.693	0.52
191_G	195_L	0.692	0.52
110_G	161_T	0.692	0.52
249_F	252_M	0.689	0.51
59_E	156_L	0.687	0.51
184_F	187_K	0.683	0.51
203_L	207_W	0.683	0.51
51_R	65_I	0.680	0.50
70_E	102_G	0.675	0.50
36_R	58_N	0.668	0.49
12_K	91_E	0.667	0.49
153_L	235_L	0.666	0.49
93_R	100_D	0.664	0.49
52_R	170_Y	0.663	0.49
100_D	189_T	0.663	0.49
42_F	108_K	0.662	0.48
39_A	69_L	0.657	0.48
188_L	195_L	0.656	0.48
267_G	270_V	0.654	0.48
11_K	53_L	0.648	0.47
94_A	125_G	0.647	0.47
102_G	186_Q	0.646	0.47
11_K	91_E	0.645	0.47
234_I	237_Q	0.645	0.47
122_I	175_D	0.643	0.46
31_S	235_L	0.643	0.46
212_I	235_L	0.638	0.46
53_L	82_I	0.637	0.46
58_N	71_F	0.637	0.46
53_L	94_A	0.637	0.46
117_G	125_G	0.636	0.46
90_E	201_G	0.630	0.45
29_Q	38_Q	0.630	0.45
244_P	249_F	0.628	0.45
277_A	280_L	0.628	0.45
253_W	256_R	0.626	0.45
151_F	157_V	0.626	0.45
130_V	146_G	0.626	0.45
25_S	162_R	0.625	0.45
12_K	55_P	0.623	0.44
266_V	280_L	0.621	0.44
31_S	44_F	0.620	0.44
118_V	121_P	0.619	0.44
80_A	165_G	0.619	0.44
250_A	267_G	0.618	0.44
77_F	154_F	0.613	0.43
86_T	90_E	0.613	0.43
66_R	145_L	0.612	0.43
110_G	116_A	0.610	0.43
32_W	195_L	0.610	0.43
89_L	241_G	0.609	0.43
62_K	106_G	0.609	0.43
54_Y	111_L	0.609	0.43
191_G	202_A	0.608	0.43
270_V	279_G	0.608	0.43
175_D	271_I	0.607	0.43
211_N	276_Y	0.606	0.43
121_P	237_Q	0.605	0.43
193_S	197_L	0.605	0.43
18_I	45_S	0.604	0.42
29_Q	76_P	0.604	0.42
229_T	232_Q	0.604	0.42
139_A	143_S	0.599	0.42
148_L	277_A	0.599	0.42
107_I	195_L	0.598	0.42
121_P	207_W	0.597	0.42
16_S	23_L	0.596	0.42
67_R	94_A	0.595	0.42
71_F	185_L	0.594	0.41
217_S	242_L	0.592	0.41
87_L	91_E	0.592	0.41
11_K	55_P	0.592	0.41
165_G	248_T	0.591	0.41
156_L	280_L	0.591	0.41
227_H	230_T	0.591	0.41
143_S	146_G	0.591	0.41
29_Q	34_F	0.590	0.41
41_G	132_A	0.590	0.41
118_V	156_L	0.589	0.41
206_K	241_G	0.588	0.41
75_Q	79_A	0.587	0.41
117_G	169_G	0.586	0.41
89_L	168_Y	0.585	0.41
106_G	109_V	0.584	0.40
185_L	205_N	0.584	0.40
159_L	198_F	0.582	0.40
232_Q	235_L	0.582	0.40
85_V	237_Q	0.579	0.40
125_G	128_R	0.578	0.40
130_V	201_G	0.577	0.40
79_A	83_L	0.574	0.39
261_P	265_I	0.573	0.39
48_P	278_C	0.572	0.39
140_M	215_V	0.572	0.39
84_G	201_G	0.572	0.39
96_G	101_D	0.571	0.39
29_Q	132_A	0.570	0.39
212_I	271_I	0.568	0.39
199_V	241_G	0.563	0.38
255_L	258_K	0.562	0.38
121_P	158_R	0.562	0.38
71_F	117_G	0.561	0.38
148_L	168_Y	0.560	0.38
17_D	21_V	0.559	0.38
58_N	80_A	0.557	0.38
208_T	244_P	0.557	0.38
192_A	261_P	0.556	0.38
75_Q	129_P	0.555	0.38
34_F	39_A	0.554	0.38
105_N	260_N	0.554	0.38
107_I	177_V	0.554	0.38
11_K	258_K	0.554	0.38
164_Y	168_Y	0.549	0.37
217_S	230_T	0.549	0.37
122_I	149_L	0.549	0.37
139_A	203_L	0.549	0.37
153_L	269_F	0.548	0.37
163_Y	166_V	0.548	0.37
14_T	91_E	0.547	0.37
213_P	230_T	0.547	0.37
23_L	26_N	0.547	0.37
47_V	61_R	0.546	0.37
230_T	280_L	0.545	0.37
17_D	49_A	0.544	0.37
62_K	65_I	0.544	0.37
210_V	271_I	0.541	0.36
29_Q	204_V	0.540	0.36
82_I	86_T	0.540	0.36
254_L	258_K	0.539	0.36
37_M	75_Q	0.538	0.36
214_L	280_L	0.537	0.36
89_L	224_G	0.536	0.36
56_E	62_K	0.535	0.36
73_N	196_G	0.534	0.36
28_F	123_F	0.533	0.35
31_S	116_A	0.530	0.35
238_L	258_K	0.530	0.35
50_I	56_E	0.529	0.35
56_E	61_R	0.528	0.35
68_H	110_G	0.527	0.35
102_G	256_R	0.527	0.35
145_L	149_L	0.527	0.35
15_Q	188_L	0.525	0.35
71_F	104_I	0.523	0.35
94_A	126_T	0.522	0.34
208_T	248_T	0.521	0.34
117_G	133_A	0.521	0.34
63_Q	214_L	0.521	0.34
137_G	150_F	0.519	0.34
133_A	158_R	0.517	0.34
148_L	246_L	0.514	0.34
88_A	176_I	0.513	0.34
130_V	242_L	0.512	0.34
138_I	237_Q	0.510	0.33
199_V	240_P	0.510	0.33
134_L	198_F	0.509	0.33
32_W	261_P	0.508	0.33
229_T	233_T	0.508	0.33
72_F	115_L	0.507	0.33
50_I	55_P	0.506	0.33
46_M	52_R	0.506	0.33
75_Q	116_A	0.506	0.33
187_K	272_G	0.505	0.33
84_G	90_E	0.505	0.33
22_F	26_N	0.505	0.33
9_T	236_D	0.504	0.33
143_S	205_N	0.503	0.33
55_P	61_R	0.501	0.32
32_W	77_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
4rp9A	2	0.1943	24.9	0.971	Contact Map
4afiA	2	0.265	19.1	0.972	Contact Map
1ashA	1	0.4099	11.7	0.975	Contact Map
2jttC	1	0.1095	7.3	0.977	Contact Map
3pf6A	2	0.1908	6.6	0.977	Contact Map
5by8A	1	0.2297	5.4	0.978	Contact Map
4b19A	1	0.1025	5.1	0.979	Contact Map
1t0fC	1	0.1731	4.4	0.979	Contact Map
3k9fC	1	0.2403	3.8	0.98	Contact Map
3g5sA	1	0.2827	3.8	0.98	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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