YDFR - BACSU - GREMLIN Contacts

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YDFR - UPF0702 transmembrane protein YdfR

UniProt:	P96696	Sequences: MNRLPFGYIKLRLAGRKANPMTNLIHHWSGGSMNFTWESLVLIVAGVILLRISGRKSIAQMTSTQTVVMISIGTIIVQPIIEYSLFKTLIAAAIFTSTLIVMEWIQMKSNTIEKMLTGKAKIVIENGQLHIENLKKMRLTADQLEMQLRLHGVTAIQDVKIATLEANGQLGIELTDDAKPLTVRDLKKLIHPDFINKDGQAQSGNQNIFDEVGKKNKKNVPKKLH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	225 (165)
Sequences:	206 (176)
Seq/√Len:	13.7

ECOLI - YCAP
BACSU - YDFR YDFS YETF YKJA YRBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
181_L	186_L	3.834	1.00
125_E	130_H	3.365	0.99
45_A	89_L	2.890	0.96
72_I	99_L	2.665	0.94
74_T	91_A	2.517	0.92
129_L	144_L	2.488	0.92
80_I	123_V	2.422	0.91
178_A	184_R	2.356	0.89
124_I	159_V	2.276	0.88
65_Q	77_V	1.958	0.78
40_L	128_Q	1.913	0.76
192_P	196_N	1.887	0.75
112_I	134_L	1.885	0.75
160_K	179_K	1.818	0.73
123_V	137_M	1.817	0.73
35_F	81_I	1.811	0.72
117_T	143_Q	1.783	0.71
108_K	142_D	1.781	0.71
136_K	148_L	1.733	0.69
126_N	135_K	1.728	0.69
186_L	190_I	1.722	0.68
129_L	181_L	1.691	0.67
36_T	166_A	1.683	0.67
112_I	135_K	1.659	0.65
74_T	92_A	1.653	0.65
68_V	154_T	1.641	0.64
55_R	103_E	1.607	0.63
71_S	74_T	1.587	0.62
43_I	74_T	1.570	0.61
108_K	120_A	1.554	0.60
70_I	79_P	1.550	0.60
48_I	186_L	1.540	0.59
123_V	170_L	1.526	0.59
71_S	91_A	1.515	0.58
48_I	115_M	1.507	0.58
125_E	133_N	1.490	0.57
153_V	172_I	1.451	0.55
69_M	73_G	1.434	0.54
72_I	106_Q	1.408	0.52
92_A	152_G	1.381	0.51
50_L	103_E	1.380	0.51
139_L	157_Q	1.362	0.50
55_R	121_K	1.361	0.50
85_L	197_K	1.347	0.49
38_E	81_I	1.340	0.49
60_Q	73_G	1.322	0.48
186_L	195_I	1.319	0.48
101_V	192_P	1.286	0.46
36_T	52_I	1.280	0.46
58_I	70_I	1.273	0.45
75_I	82_E	1.268	0.45
156_I	169_Q	1.261	0.45
128_Q	176_D	1.260	0.44
85_L	93_A	1.227	0.43
181_L	185_D	1.214	0.42
94_I	132_E	1.212	0.42
123_V	147_Q	1.197	0.41
61_M	117_T	1.184	0.40
102_M	114_K	1.177	0.40
79_P	88_T	1.172	0.40
191_H	194_F	1.164	0.39
63_S	109_S	1.164	0.39
79_P	103_E	1.160	0.39
122_I	197_K	1.154	0.39
40_L	120_A	1.151	0.39
75_I	95_F	1.150	0.39
101_V	111_T	1.145	0.38
87_K	93_A	1.144	0.38
76_I	92_A	1.135	0.38
69_M	77_V	1.132	0.38
173_E	179_K	1.131	0.38
57_S	69_M	1.129	0.38
102_M	164_L	1.113	0.37
61_M	80_I	1.097	0.36
65_Q	117_T	1.094	0.36
61_M	138_R	1.094	0.36
122_I	128_Q	1.089	0.36
80_I	154_T	1.085	0.35
60_Q	158_D	1.082	0.35
74_T	81_I	1.077	0.35
134_L	177_D	1.073	0.35
179_K	183_V	1.065	0.34
55_R	167_N	1.065	0.34
88_T	150_L	1.046	0.34
42_L	153_V	1.045	0.34
183_V	186_L	1.044	0.33
177_D	187_K	1.044	0.33
40_L	178_A	1.042	0.33
147_Q	152_G	1.013	0.32
157_Q	184_R	1.010	0.32
162_A	170_L	1.009	0.32
75_I	181_L	0.998	0.31
74_T	77_V	0.985	0.31
130_H	133_N	0.983	0.31
80_I	92_A	0.975	0.30
71_S	80_I	0.965	0.30
153_V	188_K	0.963	0.30
56_K	172_I	0.962	0.30
120_A	163_T	0.958	0.30
104_W	196_N	0.956	0.29
101_V	133_N	0.948	0.29
145_E	171_G	0.948	0.29
61_M	173_E	0.947	0.29
99_L	174_L	0.939	0.29
43_I	98_T	0.938	0.29
68_V	123_V	0.930	0.28
57_S	146_M	0.925	0.28
81_I	91_A	0.920	0.28
124_I	153_V	0.915	0.28
132_E	197_K	0.910	0.27
56_K	95_F	0.902	0.27
63_S	121_K	0.898	0.27
35_F	71_S	0.897	0.27
94_I	133_N	0.897	0.27
52_I	187_K	0.894	0.27
92_A	143_Q	0.894	0.27
187_K	190_I	0.883	0.26
85_L	188_K	0.878	0.26
60_Q	79_P	0.871	0.26
41_V	114_K	0.871	0.26
89_L	132_E	0.865	0.26
50_L	88_T	0.863	0.25
62_T	75_I	0.859	0.25
124_I	148_L	0.859	0.25
109_S	112_I	0.856	0.25
41_V	89_L	0.853	0.25
158_D	178_A	0.848	0.25
80_I	84_S	0.844	0.25
72_I	157_Q	0.838	0.24
45_A	107_M	0.833	0.24
188_K	194_F	0.816	0.24
34_N	38_E	0.809	0.23
41_V	139_L	0.806	0.23
93_A	109_S	0.805	0.23
154_T	173_E	0.798	0.23
45_A	93_A	0.795	0.23
124_I	156_I	0.792	0.23
67_V	136_K	0.792	0.23
102_M	190_I	0.786	0.22
160_K	176_D	0.774	0.22
79_P	145_E	0.768	0.22
91_A	143_Q	0.765	0.22
83_Y	96_T	0.765	0.22
113_E	120_A	0.760	0.21
34_N	153_V	0.757	0.21
106_Q	156_I	0.754	0.21
192_P	195_I	0.753	0.21
75_I	183_V	0.753	0.21
60_Q	69_M	0.749	0.21
119_K	147_Q	0.746	0.21
45_A	170_L	0.743	0.21
131_I	189_L	0.740	0.21
123_V	161_I	0.737	0.21
70_I	135_K	0.737	0.21
96_T	107_M	0.735	0.21
141_A	170_L	0.732	0.20
46_G	88_T	0.729	0.20
76_I	82_E	0.726	0.20
123_V	173_E	0.724	0.20
139_L	164_L	0.721	0.20
113_E	145_E	0.718	0.20
109_S	119_K	0.718	0.20
105_I	179_K	0.717	0.20
102_M	136_K	0.715	0.20
58_I	68_V	0.711	0.20
48_I	93_A	0.709	0.20
178_A	181_L	0.708	0.20
36_T	151_H	0.708	0.20
114_K	119_K	0.706	0.20
192_P	197_K	0.706	0.20
101_V	176_D	0.702	0.19
83_Y	126_N	0.697	0.19
160_K	173_E	0.693	0.19
84_S	146_M	0.688	0.19
136_K	142_D	0.686	0.19
55_R	66_T	0.685	0.19
62_T	73_G	0.682	0.19
44_V	101_V	0.677	0.19
53_S	68_V	0.676	0.19
148_L	153_V	0.673	0.19
121_K	151_H	0.673	0.19
145_E	158_D	0.672	0.18
33_M	160_K	0.670	0.18
33_M	94_I	0.670	0.18
99_L	171_G	0.666	0.18
77_V	88_T	0.664	0.18
105_I	123_V	0.657	0.18
44_V	90_I	0.656	0.18
65_Q	103_E	0.652	0.18
77_V	84_S	0.651	0.18
38_E	84_S	0.651	0.18
163_T	174_L	0.649	0.18
63_S	115_M	0.649	0.18
50_L	163_T	0.641	0.17
126_N	174_L	0.639	0.17
183_V	193_D	0.637	0.17
58_I	142_D	0.634	0.17
62_T	163_T	0.630	0.17
163_T	171_G	0.627	0.17
50_L	118_G	0.625	0.17
64_T	143_Q	0.622	0.17
40_L	155_A	0.614	0.17
47_V	76_I	0.612	0.17
38_E	76_I	0.611	0.17
85_L	196_N	0.610	0.17
47_V	52_I	0.609	0.17
128_Q	170_L	0.608	0.16
92_A	153_V	0.607	0.16
95_F	183_V	0.605	0.16
71_S	92_A	0.605	0.16
116_L	123_V	0.596	0.16
75_I	91_A	0.594	0.16
43_I	71_S	0.593	0.16
52_I	126_N	0.591	0.16
82_E	193_D	0.589	0.16
49_L	121_K	0.589	0.16
53_S	134_L	0.589	0.16
177_D	186_L	0.584	0.16
162_A	172_I	0.583	0.16
46_G	96_T	0.582	0.16
42_L	80_I	0.580	0.16
56_K	66_T	0.579	0.16
73_G	78_Q	0.573	0.15
194_F	197_K	0.571	0.15
148_L	159_V	0.570	0.15
40_L	176_D	0.568	0.15
151_H	188_K	0.568	0.15
74_T	155_A	0.560	0.15
36_T	97_S	0.556	0.15
100_I	197_K	0.556	0.15
178_A	185_D	0.554	0.15
73_G	150_L	0.550	0.15
44_V	123_V	0.550	0.15
129_L	196_N	0.546	0.15
134_L	139_L	0.545	0.15
78_Q	103_E	0.542	0.15
41_V	91_A	0.540	0.15
39_S	43_I	0.536	0.14
67_V	86_F	0.535	0.14
58_I	77_V	0.531	0.14
70_I	170_L	0.529	0.14
48_I	96_T	0.520	0.14
85_L	169_Q	0.513	0.14
115_M	125_E	0.511	0.14
67_V	167_N	0.510	0.14
89_L	151_H	0.510	0.14
173_E	182_T	0.505	0.14
126_N	187_K	0.500	0.14

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	0.4711	99.9	0.676	Contact Map
3mxnA	1	0.5867	12.1	0.962	Contact Map
3okfA	3	0.7467	10.6	0.963	Contact Map
1nv8A	1	0.3867	7.8	0.965	Contact Map
4bpeO	1	0.4711	6.4	0.967	Contact Map
3gdeA	1	0.6533	6.1	0.967	Contact Map
1ujnA	2	0.7289	5.4	0.968	Contact Map
2l01A	2	0.3333	5.3	0.968	Contact Map
4dbgB	1	0.4267	5.1	0.968	Contact Map
4ujpO	1	0.4489	5.1	0.968	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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