YDFS - BACSU - GREMLIN Contacts

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YDFS - UPF0702 transmembrane protein YdfS

UniProt:	P96697	Sequences: MIELEVVIRTVASFGLLLIAERILGKQTISQMTIFDFIAAITLGAIAAGLAYNTSIKPHNMAISFSIFVLTIFLISFLSIKNRKLRKFFAGDPTVLIQNGKILESNMRKMRYTLDYLNQQLREKEIFNIEEVLFAILETNGQLTVLRKPQFRHVTKQDLMIAVNQEQRLPIELIMDGEIIENNLKQNRLTESWLLEELRKRDIKVKETVYAVLLGNGDIYVDQYKDHISVPMDKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	235 (221)
Sequences:	1709 (1380)
Seq/√Len:	92.8

ECOLI - YCAP
BACSU - YDFS YETF YKJA YRBG YDFR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
197_E	200_K	7.219	1.00
181_E	191_E	7.020	1.00
131_E	151_F	4.050	1.00
94_T	106_N	3.769	1.00
203_I	208_T	3.537	1.00
126_I	147_R	3.504	1.00
154_V	159_L	3.329	1.00
26_K	94_T	3.219	1.00
85_L	89_F	3.105	1.00
87_K	92_D	2.797	1.00
128_N	131_E	2.637	1.00
203_I	223_Q	2.497	1.00
103_L	106_N	2.469	1.00
94_T	110_M	2.450	1.00
151_F	157_Q	2.316	1.00
189_L	193_W	2.297	1.00
179_I	205_V	2.277	1.00
98_Q	103_L	2.250	1.00
179_I	194_L	2.211	1.00
16_L	62_A	2.182	1.00
156_K	163_V	2.157	1.00
123_E	142_Q	2.107	1.00
126_I	132_V	2.089	1.00
174_I	211_A	2.017	1.00
121_L	132_V	1.940	1.00
99_N	133_L	1.937	1.00
20_A	69_V	1.890	1.00
7_V	63_I	1.869	1.00
214_L	218_D	1.855	1.00
198_L	203_I	1.830	1.00
127_F	146_L	1.827	1.00
102_I	117_L	1.798	1.00
97_I	129_I	1.795	1.00
208_T	211_A	1.739	1.00
121_L	145_V	1.724	1.00
97_I	117_L	1.720	1.00
191_E	195_L	1.715	1.00
131_E	147_R	1.691	1.00
112_Y	120_Q	1.689	1.00
37_F	40_A	1.633	1.00
184_L	193_W	1.600	1.00
192_S	196_E	1.580	1.00
201_R	221_V	1.546	1.00
156_K	161_I	1.538	1.00
198_L	208_T	1.528	1.00
184_L	194_L	1.526	1.00
28_T	40_A	1.521	1.00
179_I	193_W	1.514	1.00
173_L	213_L	1.511	1.00
96_L	137_L	1.487	1.00
132_V	145_V	1.469	1.00
132_V	135_A	1.466	1.00
150_Q	157_Q	1.463	1.00
211_A	221_V	1.452	1.00
207_E	223_Q	1.438	0.99
179_I	195_L	1.431	0.99
154_V	161_I	1.416	0.99
86_R	115_D	1.415	0.99
37_F	42_T	1.338	0.99
7_V	67_I	1.306	0.99
13_S	51_A	1.304	0.99
179_I	184_L	1.292	0.99
133_L	148_K	1.277	0.99
104_E	209_V	1.275	0.99
128_N	212_V	1.255	0.99
193_W	197_E	1.236	0.98
106_N	109_K	1.233	0.98
83_R	87_K	1.232	0.98
198_L	202_D	1.222	0.98
123_E	140_N	1.216	0.98
78_L	85_L	1.166	0.98
86_R	113_T	1.165	0.98
104_E	222_D	1.161	0.98
173_L	219_I	1.144	0.97
13_S	68_F	1.142	0.97
171_I	183_N	1.127	0.97
174_I	208_T	1.116	0.97
63_I	67_I	1.115	0.97
199_R	204_K	1.084	0.96
114_L	209_V	1.082	0.96
149_P	156_K	1.081	0.96
12_A	58_P	1.081	0.96
184_L	189_L	1.074	0.96
42_T	45_A	1.072	0.96
172_E	175_M	1.070	0.96
102_I	129_I	1.068	0.96
107_M	117_L	1.067	0.96
126_I	145_V	1.062	0.96
10_T	67_I	1.062	0.96
147_R	152_R	1.044	0.96
14_F	71_T	1.028	0.95
211_A	219_I	1.012	0.95
53_N	56_I	1.011	0.95
197_E	201_R	1.009	0.95
21_E	42_T	0.995	0.94
153_H	156_K	0.991	0.94
75_I	89_F	0.990	0.94
204_K	207_E	0.989	0.94
101_K	222_D	0.989	0.94
104_E	224_Y	0.988	0.94
110_M	137_L	0.987	0.94
174_I	205_V	0.978	0.94
49_G	52_Y	0.972	0.94
74_L	78_L	0.969	0.93
120_Q	143_L	0.962	0.93
159_L	162_A	0.956	0.93
114_L	175_M	0.954	0.93
96_L	112_Y	0.954	0.93
51_A	68_F	0.950	0.93
6_V	60_N	0.950	0.93
40_A	44_G	0.944	0.92
154_V	158_D	0.944	0.92
62_A	66_S	0.944	0.92
39_A	68_F	0.934	0.92
125_E	147_R	0.931	0.92
34_I	42_T	0.928	0.92
28_T	37_F	0.917	0.91
155_T	159_L	0.916	0.91
4_L	8_I	0.904	0.91
12_A	16_L	0.902	0.91
152_R	167_Q	0.891	0.90
10_T	52_Y	0.883	0.90
18_L	35_F	0.879	0.90
198_L	219_I	0.877	0.89
10_T	72_I	0.873	0.89
190_T	193_W	0.871	0.89
18_L	44_G	0.868	0.89
80_I	113_T	0.866	0.89
112_Y	116_Y	0.853	0.88
192_S	195_L	0.853	0.88
96_L	107_M	0.849	0.88
11_V	71_T	0.849	0.88
173_L	194_L	0.848	0.88
198_L	221_V	0.847	0.88
172_E	210_Y	0.846	0.88
15_G	71_T	0.842	0.87
14_F	75_I	0.836	0.87
149_P	152_R	0.834	0.87
195_L	199_R	0.832	0.87
19_I	88_F	0.830	0.87
46_I	65_F	0.829	0.87
93_P	136_I	0.829	0.87
97_I	135_A	0.829	0.87
112_Y	137_L	0.822	0.86
96_L	123_E	0.822	0.86
22_R	111_R	0.818	0.86
180_I	183_N	0.813	0.86
182_N	185_K	0.808	0.85
39_A	72_I	0.806	0.85
108_R	157_Q	0.806	0.85
93_P	134_F	0.804	0.85
29_I	32_M	0.798	0.84
47_A	57_K	0.787	0.84
21_E	40_A	0.780	0.83
82_N	85_L	0.778	0.83
26_K	110_M	0.778	0.83
45_A	49_G	0.772	0.82
147_R	153_H	0.770	0.82
133_L	149_P	0.756	0.81
124_K	142_Q	0.756	0.81
97_I	121_L	0.751	0.81
49_G	53_N	0.750	0.81
181_E	185_K	0.749	0.81
213_L	218_D	0.749	0.81
95_V	136_I	0.748	0.80
34_I	40_A	0.747	0.80
96_L	117_L	0.746	0.80
150_Q	163_V	0.742	0.80
21_E	37_F	0.739	0.80
119_Q	139_T	0.736	0.79
98_Q	186_Q	0.727	0.79
50_L	61_M	0.722	0.78
51_A	72_I	0.721	0.78
69_V	73_F	0.721	0.78
33_T	36_D	0.720	0.78
24_L	73_F	0.717	0.78
201_R	219_I	0.717	0.78
156_K	164_N	0.715	0.77
198_L	205_V	0.714	0.77
136_I	169_L	0.713	0.77
27_Q	30_S	0.710	0.77
24_L	76_S	0.707	0.77
176_D	224_Y	0.702	0.76
18_L	22_R	0.698	0.76
31_Q	37_F	0.695	0.75
28_T	32_M	0.691	0.75
137_L	143_L	0.689	0.75
21_E	34_I	0.688	0.75
31_Q	41_I	0.688	0.75
45_A	52_Y	0.687	0.75
43_L	48_A	0.686	0.74
20_A	65_F	0.685	0.74
36_D	110_M	0.682	0.74
84_K	87_K	0.682	0.74
25_G	41_I	0.682	0.74
194_L	197_E	0.680	0.74
51_A	57_K	0.676	0.73
22_R	38_I	0.675	0.73
24_L	39_A	0.671	0.73
14_F	22_R	0.671	0.73
115_D	175_M	0.664	0.72
128_N	214_L	0.660	0.72
102_I	107_M	0.658	0.71
154_V	164_N	0.658	0.71
39_A	76_S	0.657	0.71
93_P	169_L	0.656	0.71
44_G	72_I	0.656	0.71
45_A	64_S	0.655	0.71
34_I	39_A	0.655	0.71
22_R	139_T	0.654	0.71
27_Q	72_I	0.652	0.71
22_R	37_F	0.652	0.71
156_K	160_M	0.650	0.70
30_S	34_I	0.648	0.70
6_V	187_N	0.647	0.70
68_F	212_V	0.646	0.70
13_S	48_A	0.644	0.70
19_I	162_A	0.641	0.69
30_S	72_I	0.639	0.69
16_L	63_I	0.635	0.69
32_M	120_Q	0.631	0.68
150_Q	166_E	0.629	0.68
113_T	116_Y	0.629	0.68
41_I	44_G	0.628	0.68
153_H	163_V	0.627	0.68
15_G	19_I	0.623	0.67
38_I	91_G	0.623	0.67
39_A	45_A	0.622	0.67
44_G	52_Y	0.618	0.67
163_V	166_E	0.614	0.66
90_A	116_Y	0.609	0.65
98_Q	101_K	0.607	0.65
48_A	52_Y	0.607	0.65
70_L	185_K	0.601	0.64
135_A	174_I	0.600	0.64
30_S	44_G	0.599	0.64
44_G	49_G	0.598	0.64
40_A	43_L	0.598	0.64
18_L	89_F	0.597	0.64
34_I	37_F	0.595	0.64
42_T	52_Y	0.595	0.64
32_M	90_A	0.595	0.64
83_R	180_I	0.593	0.63
195_L	205_V	0.593	0.63
181_E	206_K	0.591	0.63
83_R	178_E	0.590	0.63
173_L	187_N	0.590	0.63
117_L	135_A	0.584	0.62
52_Y	72_I	0.582	0.62
68_F	72_I	0.582	0.62
40_A	49_G	0.580	0.62
32_M	112_Y	0.578	0.61
77_F	81_K	0.577	0.61
30_S	76_S	0.576	0.61
105_S	108_R	0.576	0.61
83_R	115_D	0.576	0.61
33_T	116_Y	0.575	0.61
184_L	191_E	0.573	0.61
18_L	71_T	0.573	0.61
73_F	111_R	0.573	0.61
131_E	148_K	0.572	0.61
192_S	204_K	0.567	0.60
117_L	139_T	0.567	0.60
129_I	210_Y	0.567	0.60
43_L	117_L	0.566	0.60
45_A	90_A	0.566	0.60
80_I	115_D	0.566	0.60
68_F	76_S	0.565	0.60
17_L	20_A	0.563	0.59
173_L	193_W	0.560	0.59
95_V	147_R	0.558	0.59
57_K	60_N	0.557	0.59
182_N	186_Q	0.557	0.59
78_L	185_K	0.556	0.58
69_V	120_Q	0.555	0.58
4_L	125_E	0.554	0.58
96_L	135_A	0.554	0.58
53_N	90_A	0.552	0.58
190_T	204_K	0.550	0.58
46_I	51_A	0.550	0.58
77_F	111_R	0.549	0.58
155_T	160_M	0.549	0.58
76_S	140_N	0.548	0.57
10_T	39_A	0.547	0.57
28_T	43_L	0.546	0.57
114_L	210_Y	0.542	0.57
28_T	36_D	0.542	0.57
23_I	73_F	0.542	0.57
33_T	90_A	0.540	0.56
149_P	166_E	0.539	0.56
7_V	164_N	0.538	0.56
70_L	74_L	0.538	0.56
37_F	49_G	0.538	0.56
79_S	85_L	0.534	0.55
74_L	192_S	0.534	0.55
169_L	180_I	0.533	0.55
53_N	76_S	0.532	0.55
27_Q	64_S	0.532	0.55
13_S	34_I	0.532	0.55
12_A	56_I	0.531	0.55
37_F	41_I	0.529	0.55
154_V	157_Q	0.529	0.55
45_A	72_I	0.529	0.55
15_G	23_I	0.527	0.55
158_D	161_I	0.527	0.55
23_I	162_A	0.527	0.55
188_R	191_E	0.526	0.54
13_S	58_P	0.526	0.54
13_S	50_L	0.525	0.54
194_L	208_T	0.525	0.54
99_N	163_V	0.524	0.54
5_E	129_I	0.523	0.54
31_Q	40_A	0.522	0.54
40_A	50_L	0.522	0.54
45_A	55_S	0.518	0.53
125_E	153_H	0.514	0.53
48_A	51_A	0.513	0.53
39_A	49_G	0.513	0.53
187_N	213_L	0.512	0.52
24_L	28_T	0.511	0.52
46_I	140_N	0.507	0.52
188_R	193_W	0.506	0.52
128_N	151_F	0.506	0.52
175_M	210_Y	0.505	0.51
70_L	192_S	0.504	0.51
83_R	218_D	0.504	0.51
28_T	116_Y	0.503	0.51
17_L	35_F	0.502	0.51
112_Y	212_V	0.501	0.51
47_A	101_K	0.501	0.51
32_M	118_N	0.501	0.51
193_W	208_T	0.500	0.51

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
3c6fA	4	0.583	100	0.39	Contact Map
4dynA	3	0.3489	12.8	0.963	Contact Map
2jo7A	1	0.4936	10.3	0.964	Contact Map
2pwjA	2	0.6085	7.6	0.966	Contact Map
4b4aA	1	0.3149	7.6	0.966	Contact Map
2kncA	1	0.2298	5.5	0.968	Contact Map
2x8xX	1	0.6596	5.5	0.968	Contact Map
3wkvA	3	0.417	5.5	0.969	Contact Map
3eviA	2	0.4638	5.3	0.969	Contact Map
4ltoA	3	0.4979	4.9	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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