YOMD - BACSU - GREMLIN Contacts

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YOMD - SPBc2 prophage-derived uncharacterized protein YomD

UniProt:	O31981	Sequences: MARKISDYHLKKREETQKKFIDLLAQNNYIHISGDMVNSKTKVKVRCRHNHTWQVNYEHFKKGTRCPECRIIEGSLKKRLNISTVKSRYALKGYEILSTYKNCHSKLKAKCPEGHIWEHLPSNFFKGEECFQCKGAKKYTVECAQAAFSDRGFIPLFDTYHHNKENLPFLCKEHIDLGVQYAPLHNMVRGLANCRKCYLLLFTGENSSRWKGGISSLNKTLREAVYEVWTKPSLEKYSFKCAITNSTKDLHVHHYKKNFSEIVKEALSNLSFEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	274 (217)
Sequences:	145 (142)
Seq/√Len:	9.6

BACSU - YOMD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_W	117_W	4.277	0.99
168_P	171_C	3.540	0.97
167_L	170_L	3.517	0.97
194_C	201_L	3.467	0.96
60_F	65_R	3.441	0.96
47_C	111_C	3.309	0.95
141_V	148_F	3.299	0.95
195_R	202_F	3.216	0.94
178_G	181_Y	3.172	0.94
202_F	205_E	2.870	0.90
168_P	172_K	2.821	0.89
182_A	186_N	2.821	0.89
45_V	109_A	2.672	0.86
180_Q	216_S	2.619	0.85
24_L	32_I	2.613	0.85
124_F	129_E	2.592	0.85
96_I	99_T	2.540	0.83
165_E	168_P	2.333	0.78
216_S	219_K	2.216	0.74
93_G	111_C	2.197	0.73
102_N	105_S	2.179	0.72
60_F	124_F	2.029	0.67
140_T	179_V	1.919	0.62
167_L	171_C	1.913	0.62
102_N	114_G	1.899	0.61
66_C	69_C	1.867	0.60
38_N	41_T	1.852	0.59
123_N	128_E	1.848	0.59
206_N	216_S	1.768	0.56
205_E	212_G	1.754	0.55
216_S	221_L	1.740	0.54
165_E	170_L	1.739	0.54
136_A	140_T	1.723	0.54
161_H	168_P	1.714	0.53
198_Y	201_L	1.689	0.52
166_N	185_H	1.684	0.52
169_F	184_L	1.676	0.51
197_C	201_L	1.666	0.51
130_C	133_C	1.643	0.50
20_F	57_Y	1.631	0.49
195_R	201_L	1.628	0.49
167_L	172_K	1.625	0.49
167_L	176_D	1.620	0.49
180_Q	206_N	1.604	0.48
45_V	53_W	1.593	0.48
205_E	209_R	1.567	0.47
38_N	186_N	1.534	0.45
148_F	169_F	1.523	0.45
26_Q	29_Y	1.520	0.44
181_Y	184_L	1.491	0.43
44_K	52_T	1.417	0.40
209_R	214_I	1.409	0.40
169_F	177_L	1.381	0.38
103_C	186_N	1.369	0.38
145_Q	155_P	1.357	0.37
69_C	133_C	1.354	0.37
69_C	130_C	1.354	0.37
192_A	196_K	1.346	0.37
51_H	115_H	1.344	0.37
142_E	145_Q	1.330	0.36
167_L	209_R	1.322	0.36
66_C	133_C	1.318	0.36
66_C	130_C	1.318	0.36
208_S	212_G	1.296	0.35
65_R	129_E	1.286	0.34
32_I	96_I	1.272	0.34
183_P	190_G	1.270	0.34
171_C	175_I	1.258	0.33
177_L	181_Y	1.256	0.33
123_N	154_I	1.248	0.33
190_G	198_Y	1.247	0.33
147_A	225_V	1.224	0.32
55_V	132_Q	1.220	0.32
184_L	205_E	1.218	0.32
204_G	212_G	1.207	0.31
56_N	63_G	1.202	0.31
94_Y	111_C	1.194	0.31
93_G	108_K	1.173	0.30
109_A	117_W	1.165	0.30
169_F	185_H	1.156	0.29
141_V	178_G	1.154	0.29
191_L	194_C	1.152	0.29
88_R	111_C	1.130	0.28
168_P	173_E	1.112	0.28
191_L	195_R	1.111	0.28
218_N	221_L	1.098	0.27
50_N	114_G	1.097	0.27
191_L	202_F	1.092	0.27
26_Q	58_E	1.091	0.27
47_C	69_C	1.091	0.27
105_S	196_K	1.078	0.27
57_Y	121_P	1.071	0.26
46_R	52_T	1.062	0.26
177_L	180_Q	1.061	0.26
171_C	174_H	1.046	0.25
180_Q	185_H	1.039	0.25
56_N	59_H	1.037	0.25
34_G	47_C	1.034	0.25
141_V	181_Y	1.020	0.25
129_E	171_C	1.020	0.25
92_K	108_K	1.016	0.24
188_V	213_G	1.005	0.24
145_Q	149_S	0.991	0.24
132_Q	149_S	0.984	0.23
111_C	129_E	0.976	0.23
166_N	184_L	0.975	0.23
111_C	133_C	0.974	0.23
111_C	130_C	0.974	0.23
22_D	165_E	0.966	0.23
80_L	84_T	0.959	0.23
141_V	144_A	0.956	0.22
17_Q	21_I	0.941	0.22
126_K	150_D	0.938	0.22
170_L	173_E	0.928	0.22
184_L	201_L	0.922	0.21
144_A	179_V	0.920	0.21
72_I	200_L	0.916	0.21
190_G	194_C	0.911	0.21
30_I	60_F	0.904	0.21
208_S	215_S	0.898	0.21
169_F	176_D	0.898	0.21
154_I	159_T	0.897	0.21
191_L	201_L	0.896	0.21
148_F	181_Y	0.896	0.21
67_P	93_G	0.888	0.20
205_E	217_L	0.880	0.20
59_H	101_K	0.875	0.20
126_K	189_R	0.875	0.20
91_L	121_P	0.874	0.20
16_T	19_K	0.868	0.20
20_F	121_P	0.863	0.20
54_Q	64_T	0.863	0.20
47_C	130_C	0.863	0.20
47_C	133_C	0.863	0.20
166_N	176_D	0.857	0.20
186_N	189_R	0.855	0.19
24_L	28_N	0.853	0.19
169_F	183_P	0.852	0.19
194_C	202_F	0.848	0.19
43_V	143_C	0.843	0.19
43_V	52_T	0.838	0.19
102_N	189_R	0.838	0.19
140_T	147_A	0.832	0.19
87_S	110_K	0.830	0.19
56_N	83_S	0.829	0.19
88_R	129_E	0.828	0.19
203_T	207_S	0.826	0.19
210_W	233_S	0.826	0.19
142_E	173_E	0.825	0.19
53_W	109_A	0.822	0.19
219_K	225_V	0.818	0.18
185_H	218_N	0.816	0.18
148_F	178_G	0.809	0.18
185_H	216_S	0.804	0.18
190_G	201_L	0.803	0.18
160_Y	168_P	0.802	0.18
24_L	96_I	0.796	0.18
45_V	144_A	0.796	0.18
28_N	47_C	0.790	0.18
59_H	62_K	0.787	0.18
36_M	61_K	0.782	0.18
143_C	148_F	0.781	0.17
178_G	184_L	0.777	0.17
121_P	125_F	0.776	0.17
176_D	201_L	0.773	0.17
50_N	209_R	0.766	0.17
34_G	40_K	0.764	0.17
55_V	60_F	0.757	0.17
38_N	59_H	0.756	0.17
187_M	190_G	0.751	0.17
45_V	124_F	0.748	0.17
55_V	110_K	0.745	0.17
52_T	73_E	0.744	0.17
63_G	196_K	0.743	0.17
114_G	200_L	0.743	0.17
72_I	77_K	0.738	0.16
23_L	121_P	0.730	0.16
90_A	93_G	0.726	0.16
64_T	164_K	0.724	0.16
42_K	123_N	0.721	0.16
62_K	126_K	0.720	0.16
153_F	215_S	0.717	0.16
32_I	45_V	0.714	0.16
90_A	124_F	0.710	0.16
32_I	93_G	0.708	0.16
170_L	180_Q	0.707	0.16
166_N	169_F	0.704	0.16
227_E	233_S	0.701	0.15
45_V	115_H	0.700	0.15
191_L	200_L	0.696	0.15
205_E	208_S	0.695	0.15
70_R	121_P	0.694	0.15
26_Q	47_C	0.692	0.15
41_T	105_S	0.690	0.15
118_E	200_L	0.688	0.15
41_T	96_I	0.687	0.15
130_C	178_G	0.686	0.15
133_C	178_G	0.686	0.15
96_I	114_G	0.682	0.15
65_R	119_H	0.681	0.15
158_D	198_Y	0.677	0.15
55_V	64_T	0.677	0.15
115_H	149_S	0.676	0.15
18_K	88_R	0.673	0.15
141_V	145_Q	0.672	0.15
88_R	108_K	0.670	0.15
141_V	179_V	0.669	0.15
40_K	54_Q	0.667	0.15
59_H	78_K	0.667	0.15
45_V	51_H	0.667	0.15
36_M	100_Y	0.662	0.15
60_F	149_S	0.662	0.15
141_V	158_D	0.662	0.15
184_L	202_F	0.661	0.15
45_V	88_R	0.657	0.14
24_L	45_V	0.657	0.14
117_W	129_E	0.651	0.14
34_G	114_G	0.642	0.14
27_N	107_L	0.634	0.14
25_A	101_K	0.632	0.14
99_T	102_N	0.631	0.14
160_Y	167_L	0.629	0.14
159_T	198_Y	0.627	0.14
84_T	102_N	0.624	0.14
49_H	191_L	0.623	0.14
69_C	111_C	0.623	0.14
24_L	34_G	0.623	0.14
39_S	119_H	0.622	0.14
59_H	73_E	0.622	0.14
47_C	93_G	0.616	0.14
177_L	212_G	0.616	0.14
93_G	97_L	0.615	0.14
39_S	105_S	0.615	0.14
47_C	66_C	0.614	0.14
42_K	54_Q	0.612	0.14
71_I	74_G	0.612	0.14
54_Q	193_N	0.608	0.13
45_V	49_H	0.608	0.13
15_E	32_I	0.607	0.13
185_H	201_L	0.604	0.13
179_V	222_R	0.604	0.13
49_H	173_E	0.604	0.13
109_A	124_F	0.603	0.13
25_A	46_R	0.601	0.13
222_R	229_W	0.601	0.13
53_W	211_K	0.601	0.13
59_H	223_E	0.599	0.13
45_V	55_V	0.597	0.13
111_C	119_H	0.594	0.13
68_E	119_H	0.593	0.13
156_L	159_T	0.592	0.13
172_K	194_C	0.591	0.13
55_V	119_H	0.590	0.13
38_N	56_N	0.590	0.13
118_E	211_K	0.589	0.13
125_F	134_K	0.587	0.13
117_W	170_L	0.586	0.13
152_G	196_K	0.583	0.13
144_A	204_G	0.581	0.13
36_M	88_R	0.579	0.13
44_K	88_R	0.579	0.13
59_H	196_K	0.578	0.13
205_E	213_G	0.577	0.13
230_T	234_L	0.574	0.13
141_V	207_S	0.572	0.13
71_I	128_E	0.570	0.13
226_Y	234_L	0.570	0.13
56_N	122_S	0.570	0.13
120_L	123_N	0.570	0.13
90_A	117_W	0.566	0.13
161_H	170_L	0.566	0.13
220_T	229_W	0.563	0.13
105_S	118_E	0.562	0.12
104_H	123_N	0.560	0.12
204_G	211_K	0.559	0.12
60_F	185_H	0.559	0.12
156_L	199_L	0.558	0.12
176_D	185_H	0.557	0.12
45_V	60_F	0.556	0.12
154_I	233_S	0.552	0.12
44_K	108_K	0.552	0.12
92_K	111_C	0.551	0.12
82_I	93_G	0.550	0.12
27_N	30_I	0.548	0.12
31_H	94_Y	0.548	0.12
32_I	114_G	0.548	0.12
147_A	231_K	0.548	0.12
137_K	208_S	0.544	0.12
193_N	213_G	0.543	0.12
121_P	202_F	0.543	0.12
53_W	65_R	0.541	0.12
86_K	164_K	0.540	0.12
22_D	74_G	0.540	0.12
21_I	61_K	0.540	0.12
19_K	22_D	0.539	0.12
171_C	190_G	0.537	0.12
117_W	122_S	0.537	0.12
129_E	144_A	0.535	0.12
143_C	147_A	0.532	0.12
21_I	46_R	0.531	0.12
68_E	88_R	0.529	0.12
41_T	57_Y	0.528	0.12
148_F	184_L	0.527	0.12
91_L	199_L	0.525	0.12
182_A	189_R	0.524	0.12
187_M	207_S	0.524	0.12
52_T	74_G	0.524	0.12
38_N	118_E	0.521	0.12
51_H	77_K	0.517	0.12
205_E	214_I	0.517	0.12
175_I	188_V	0.517	0.12
195_R	214_I	0.516	0.12
137_K	157_F	0.512	0.12
20_F	47_C	0.510	0.12
41_T	106_K	0.508	0.11
85_V	224_A	0.508	0.11
32_I	121_P	0.507	0.11
84_T	93_G	0.504	0.11
148_F	158_D	0.503	0.11
121_P	212_G	0.503	0.11
151_R	176_D	0.503	0.11
41_T	143_C	0.502	0.11
53_W	125_F	0.501	0.11
20_F	25_A	0.501	0.11
137_K	144_A	0.501	0.11
56_N	73_E	0.500	0.11

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
4oq2A	1	0.5438	97.6	0.899	Contact Map
3hrlA	1	0.3212	96.9	0.91	Contact Map
1vsrA	1	0.4234	96.7	0.912	Contact Map
3r3pA	3	0.3467	96.5	0.914	Contact Map
4parB	3	0.5657	96.4	0.915	Contact Map
1cw0A	1	0.4964	96.1	0.918	Contact Map
2k2dA	1	0.1679	87.5	0.938	Contact Map
1yuzA	2	0.2701	65	0.95	Contact Map
1lkoA	3	0.281	59.3	0.952	Contact Map
4aybP	1	0.1569	59.2	0.952	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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