YKJA - BACSU - GREMLIN Contacts

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YKJA - UPF0702 transmembrane protein YkjA

UniProt:	P49853	Sequences: MLWMVWVFLLKPVIVFSIAYILFRLAGKKAVSQMNNFDLLLTFAIGTIISEPILTSKLPMSIYYAGAFLVLYLIMSKLSLSNKWRWLLVVSPTVLIRNGDIDERGLRKERLTVNELLGKLREKGYADPADIDLAIIEETGEVSVIPKEEARAVQVRDLNMEAERNFIPIPLILDGEILDHNLKYLQKNRSWLFEKLEEKGYSPKLLSSIILGTMNARGDISLDLNTANEPQHDPYLYKPGNNN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (220)
Sequences:	1698 (1377)
Seq/√Len:	92.8

BACSU - YKJA YETF YDFS 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
195_K	198_E	6.777	1.00
179_D	189_R	6.716	1.00
130_D	150_A	4.005	1.00
93_T	105_G	3.614	1.00
201_Y	209_I	3.369	1.00
125_Y	146_P	3.322	1.00
153_V	158_L	3.284	1.00
203_P	207_S	3.129	1.00
28_K	93_T	3.068	1.00
84_W	88_L	2.936	1.00
86_W	91_S	2.606	1.00
127_D	130_D	2.570	1.00
93_T	109_E	2.364	1.00
201_Y	224_L	2.361	1.00
102_D	105_G	2.269	1.00
203_P	208_S	2.268	1.00
177_I	206_L	2.227	1.00
150_A	156_R	2.218	1.00
18_I	62_I	2.196	1.00
187_K	191_W	2.194	1.00
97_R	102_D	2.107	1.00
125_Y	131_I	2.070	1.00
122_E	141_E	2.066	1.00
177_I	192_L	2.020	1.00
22_L	69_L	1.987	1.00
120_L	131_I	1.983	1.00
155_V	162_A	1.983	1.00
172_I	212_G	1.940	1.00
98_N	132_D	1.934	1.00
9_L	63_Y	1.893	1.00
215_N	219_D	1.840	1.00
209_I	212_G	1.790	1.00
120_L	144_V	1.767	1.00
126_A	145_I	1.740	1.00
101_I	116_L	1.713	1.00
130_D	146_P	1.689	1.00
96_I	128_P	1.640	1.00
196_L	201_Y	1.628	1.00
212_G	222_L	1.625	1.00
155_V	160_M	1.623	1.00
111_L	119_K	1.612	1.00
153_V	160_M	1.606	1.00
39_L	42_T	1.597	1.00
96_I	116_L	1.584	1.00
190_S	194_E	1.545	1.00
189_R	193_F	1.543	1.00
177_I	191_W	1.505	1.00
131_I	144_V	1.492	1.00
208_S	224_L	1.489	1.00
182_L	191_W	1.483	1.00
95_L	136_I	1.458	1.00
199_K	222_L	1.457	1.00
30_A	42_T	1.450	1.00
83_K	86_W	1.444	1.00
177_I	193_F	1.436	0.99
171_L	214_M	1.430	0.99
196_L	209_I	1.416	0.99
131_I	134_A	1.409	0.99
85_R	114_N	1.396	0.99
182_L	192_L	1.386	0.99
132_D	147_K	1.319	0.99
103_E	210_I	1.316	0.99
177_I	182_L	1.314	0.99
149_E	156_R	1.304	0.99
39_L	44_A	1.298	0.99
9_L	67_A	1.261	0.99
5_V	63_Y	1.242	0.98
196_L	200_G	1.233	0.98
127_D	213_T	1.221	0.98
122_E	139_T	1.215	0.98
15_V	53_I	1.203	0.98
15_V	68_F	1.194	0.98
85_R	112_T	1.186	0.98
105_G	108_K	1.154	0.98
103_E	223_D	1.150	0.97
202_S	208_S	1.139	0.97
171_L	220_I	1.132	0.97
148_E	155_V	1.119	0.97
44_A	47_T	1.110	0.97
169_I	181_N	1.095	0.97
172_I	209_I	1.093	0.97
113_V	210_I	1.086	0.96
125_Y	144_V	1.084	0.96
191_W	195_K	1.081	0.96
78_L	84_W	1.067	0.96
182_L	187_K	1.053	0.96
170_P	173_L	1.035	0.95
101_I	128_P	1.032	0.95
106_L	116_L	1.023	0.95
195_K	199_K	1.017	0.95
103_E	225_N	1.016	0.95
196_L	220_I	1.001	0.94
23_F	44_A	1.000	0.94
124_G	146_P	0.989	0.94
12_P	54_L	0.988	0.94
146_P	151_R	0.988	0.94
6_W	10_L	0.986	0.94
95_L	106_L	0.970	0.93
16_F	71_L	0.969	0.93
12_P	67_A	0.968	0.93
95_L	111_L	0.960	0.93
119_K	142_V	0.959	0.93
149_E	164_R	0.951	0.93
212_G	220_I	0.950	0.93
146_P	152_A	0.950	0.93
30_A	39_L	0.947	0.93
80_L	112_T	0.944	0.92
42_T	46_G	0.943	0.92
53_I	68_F	0.933	0.92
41_L	68_F	0.931	0.92
100_D	223_D	0.926	0.92
197_E	202_S	0.926	0.92
172_I	206_L	0.922	0.92
153_V	157_D	0.917	0.91
51_E	54_L	0.909	0.91
109_E	136_I	0.902	0.91
111_L	115_E	0.899	0.91
36_N	44_A	0.895	0.90
24_R	110_R	0.893	0.90
196_L	222_L	0.883	0.90
188_N	191_W	0.881	0.90
20_Y	37_F	0.880	0.90
12_P	72_Y	0.875	0.89
107_R	156_R	0.873	0.89
113_V	173_L	0.868	0.89
63_Y	67_A	0.866	0.89
96_I	134_A	0.864	0.89
75_M	88_L	0.862	0.89
151_R	165_N	0.857	0.88
170_P	211_L	0.854	0.88
14_I	18_I	0.850	0.88
62_I	66_G	0.845	0.88
48_I	65_A	0.845	0.88
111_L	136_I	0.844	0.88
20_Y	46_G	0.844	0.88
14_I	60_M	0.837	0.87
196_L	206_L	0.834	0.87
92_P	133_L	0.833	0.87
152_A	155_V	0.831	0.87
190_S	193_F	0.829	0.87
180_H	183_K	0.823	0.86
31_V	34_M	0.816	0.86
74_I	78_L	0.813	0.86
95_L	116_L	0.806	0.85
47_T	51_E	0.805	0.85
171_L	192_L	0.805	0.85
149_E	162_A	0.801	0.85
123_K	141_E	0.801	0.85
199_K	220_I	0.798	0.84
16_F	75_M	0.796	0.84
136_I	142_V	0.795	0.84
41_L	72_Y	0.788	0.84
94_V	135_I	0.778	0.83
148_E	151_R	0.777	0.83
95_L	122_E	0.776	0.83
26_A	73_L	0.768	0.82
5_V	8_F	0.764	0.82
28_K	109_E	0.762	0.82
35_N	38_D	0.761	0.82
178_L	181_N	0.759	0.81
23_F	36_N	0.759	0.81
36_N	42_T	0.756	0.81
29_K	32_S	0.755	0.81
21_I	87_L	0.753	0.81
23_F	42_T	0.752	0.81
92_P	135_I	0.749	0.81
26_A	76_S	0.749	0.81
118_G	138_E	0.746	0.80
193_F	197_E	0.742	0.80
101_I	106_L	0.741	0.80
53_I	72_Y	0.736	0.79
179_D	183_K	0.735	0.79
47_T	54_L	0.734	0.79
55_T	58_L	0.732	0.79
21_I	161_E	0.732	0.79
33_Q	43_F	0.727	0.79
51_E	55_T	0.724	0.78
47_T	57_K	0.723	0.78
52_P	61_S	0.721	0.78
157_D	160_M	0.718	0.78
40_L	90_V	0.716	0.77
24_R	40_L	0.713	0.77
23_F	39_L	0.709	0.77
45_I	50_S	0.709	0.77
15_V	50_S	0.703	0.76
13_V	71_L	0.700	0.76
96_I	120_L	0.698	0.76
49_I	59_P	0.694	0.75
112_T	115_E	0.692	0.75
32_S	72_Y	0.692	0.75
127_D	215_N	0.689	0.75
81_S	108_K	0.688	0.75
70_V	183_K	0.688	0.75
97_R	184_Y	0.687	0.75
26_A	41_L	0.685	0.74
33_Q	39_L	0.683	0.74
154_Q	158_L	0.683	0.74
203_P	206_L	0.678	0.74
68_F	213_T	0.673	0.73
48_I	53_I	0.673	0.73
30_A	34_M	0.671	0.73
32_S	36_N	0.670	0.73
22_L	65_A	0.669	0.73
158_L	161_E	0.669	0.73
17_S	71_L	0.669	0.73
114_N	173_L	0.667	0.72
54_L	60_M	0.665	0.72
7_V	128_P	0.665	0.72
41_L	47_T	0.662	0.72
186_Q	191_W	0.661	0.72
29_K	72_Y	0.659	0.71
47_T	64_Y	0.658	0.71
190_S	202_S	0.656	0.71
24_R	39_L	0.655	0.71
192_L	195_K	0.646	0.70
38_D	109_E	0.645	0.70
132_D	148_E	0.641	0.69
104_R	107_R	0.640	0.69
47_T	89_V	0.638	0.69
79_S	84_W	0.638	0.69
130_D	147_K	0.632	0.68
55_T	89_V	0.631	0.68
182_L	189_R	0.628	0.68
155_V	159_N	0.627	0.68
19_A	37_F	0.627	0.68
94_V	146_P	0.626	0.68
20_Y	24_R	0.626	0.68
34_M	111_L	0.625	0.67
16_F	24_R	0.624	0.67
34_M	119_K	0.622	0.67
155_V	163_E	0.621	0.67
8_F	185_L	0.620	0.67
18_I	63_Y	0.619	0.67
85_R	89_V	0.619	0.67
124_G	152_A	0.617	0.66
116_L	134_A	0.615	0.66
46_G	72_Y	0.615	0.66
171_L	185_L	0.615	0.66
187_K	218_G	0.612	0.66
36_N	39_L	0.611	0.66
89_V	115_E	0.609	0.65
78_L	183_K	0.608	0.65
32_S	76_S	0.608	0.65
69_L	119_K	0.608	0.65
39_L	51_E	0.607	0.65
68_F	72_Y	0.606	0.65
164_R	216_A	0.599	0.64
50_S	54_L	0.597	0.64
36_N	41_L	0.595	0.64
27_G	43_F	0.594	0.64
214_M	219_D	0.594	0.64
69_L	73_L	0.593	0.63
12_P	41_L	0.593	0.63
45_I	116_L	0.590	0.63
35_N	115_E	0.589	0.63
41_L	76_S	0.589	0.63
40_L	68_F	0.587	0.63
159_N	222_L	0.583	0.62
24_R	61_S	0.582	0.62
30_A	38_D	0.581	0.62
156_R	163_E	0.580	0.62
24_R	138_E	0.580	0.62
200_G	218_G	0.580	0.62
113_V	211_L	0.579	0.62
32_S	46_G	0.579	0.62
192_L	209_I	0.577	0.61
116_L	138_E	0.575	0.61
14_I	58_L	0.574	0.61
20_Y	71_L	0.574	0.61
183_K	197_E	0.573	0.61
70_V	184_Y	0.563	0.59
34_M	89_V	0.562	0.59
42_T	45_I	0.561	0.59
97_R	100_D	0.561	0.59
135_I	167_I	0.561	0.59
174_D	225_N	0.560	0.59
127_D	165_N	0.559	0.59
25_L	73_L	0.557	0.59
43_F	46_G	0.556	0.58
199_K	219_D	0.554	0.58
70_V	74_I	0.553	0.58
54_L	72_Y	0.551	0.58
194_E	200_G	0.549	0.58
128_P	211_L	0.547	0.57
50_S	53_I	0.546	0.57
46_G	54_L	0.546	0.57
46_G	51_E	0.545	0.57
134_A	172_I	0.545	0.57
15_V	36_N	0.543	0.57
77_K	110_R	0.543	0.57
125_Y	161_E	0.542	0.57
44_A	54_L	0.541	0.56
35_N	89_V	0.539	0.56
66_G	69_L	0.536	0.56
80_L	114_N	0.536	0.56
47_T	72_Y	0.533	0.55
185_L	214_M	0.533	0.55
42_T	51_E	0.531	0.55
33_Q	42_T	0.531	0.55
41_L	51_E	0.530	0.55
15_V	51_E	0.528	0.55
171_L	191_W	0.526	0.54
89_V	112_T	0.526	0.54
14_I	66_G	0.525	0.54
154_Q	160_M	0.524	0.54
44_A	72_Y	0.522	0.54
19_A	36_N	0.522	0.54
73_L	110_R	0.520	0.54
17_S	88_L	0.519	0.53
68_F	76_S	0.516	0.53
188_N	202_S	0.515	0.53
38_D	118_G	0.515	0.53
186_Q	189_R	0.512	0.52
180_H	184_Y	0.511	0.52
87_L	135_I	0.509	0.52
18_I	66_G	0.508	0.52
6_W	124_G	0.508	0.52
19_A	22_L	0.508	0.52
29_K	54_L	0.508	0.52
180_H	207_S	0.506	0.52
39_L	43_F	0.506	0.52
37_F	201_Y	0.506	0.52
26_A	29_K	0.505	0.51
15_V	60_M	0.505	0.51
95_L	134_A	0.505	0.51
15_V	52_P	0.504	0.51
148_E	164_R	0.503	0.51
186_Q	224_L	0.502	0.51
30_A	115_E	0.502	0.51
74_I	190_S	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	0.5679	100	0.423	Contact Map
4b4aA	1	0.3086	19.5	0.961	Contact Map
4dynA	3	0.3374	6.9	0.968	Contact Map
2ma3A	1	0.3251	5.5	0.97	Contact Map
1whzA	1	0.2798	5	0.97	Contact Map
1uxcA	1	0.1564	4.5	0.971	Contact Map
4umwA	1	0.7449	4.2	0.971	Contact Map
3wkvA	3	0.4156	4.2	0.971	Contact Map
2pwjA	2	0.5802	4.2	0.971	Contact Map
1g2hA	1	0.251	4	0.972	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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