YFND - BACSU - GREMLIN Contacts

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YFND - Uncharacterized protein YfnD

UniProt:	O31542	Sequences: MSTFHFSTIVSRTHIFKLMPMIHSLHEHCDDFHLYVLCVDQKAYELLQHVPWEHVTFVQLHEMEDPELLKAKSNRTFHEYCWTLKPAFLFHVMSKWDDAEYFAHMDTDLFFFSDPARIFAENPTASLYLTDHRNSPRFMSYYDRTGRFNTGFVGAGNTKEAYEAVWQWRQDCIEFCTVEMDTERKTYGDQRYVEKWPEQFKGVHVVKSIGANTALWNIENYKVGQKDGRVYIDETPLIFYHFSGFTLVTEKEFNLCWYYRIEDEATIKMIYMPYILNLKRWIDEIQSAFPDFADGFIPKHAVPDTHFIQLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	311 (284)
Sequences:	304 (272)
Seq/√Len:	16.1

BACSU - YFND YFNF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_L	88_F	4.131	1.00
82_W	188_G	3.528	1.00
148_F	203_V	3.205	0.99
101_Y	123_P	3.145	0.99
11_S	81_C	2.942	0.98
108_D	241_H	2.847	0.98
150_T	193_V	2.837	0.98
126_S	158_T	2.831	0.98
152_F	239_F	2.760	0.97
33_H	56_T	2.725	0.97
103_A	154_G	2.628	0.96
151_G	212_N	2.561	0.95
132_H	149_N	2.537	0.95
82_W	150_T	2.435	0.94
85_K	212_N	2.310	0.92
14_H	108_D	2.297	0.92
225_Q	269_M	2.295	0.92
90_F	166_W	2.211	0.90
109_L	239_F	2.162	0.89
10_V	18_L	2.154	0.89
132_H	214_A	2.141	0.89
149_N	212_N	2.115	0.88
72_K	80_Y	2.072	0.87
191_R	194_E	1.936	0.83
107_T	150_T	1.919	0.83
93_M	97_D	1.904	0.82
57_F	147_R	1.849	0.80
82_W	107_T	1.820	0.79
90_F	169_R	1.795	0.78
82_W	193_V	1.745	0.76
195_K	199_Q	1.697	0.74
87_A	169_R	1.694	0.74
7_S	88_F	1.690	0.74
14_H	150_T	1.684	0.73
108_D	176_C	1.680	0.73
5_H	35_Y	1.655	0.72
85_K	151_G	1.643	0.71
151_G	243_S	1.636	0.71
164_A	193_V	1.632	0.71
232_I	237_L	1.628	0.71
20_P	281_W	1.622	0.70
167_Q	185_K	1.617	0.70
176_C	241_H	1.587	0.69
118_I	211_A	1.584	0.68
209_I	235_T	1.563	0.67
7_S	89_L	1.561	0.67
65_D	169_R	1.560	0.67
147_R	198_E	1.556	0.67
36_V	55_V	1.555	0.67
86_P	165_V	1.543	0.66
88_F	93_M	1.541	0.66
85_K	243_S	1.517	0.65
92_V	99_A	1.513	0.65
148_F	193_V	1.498	0.64
8_T	24_S	1.497	0.64
90_F	94_S	1.492	0.64
14_H	176_C	1.491	0.64
160_E	163_E	1.489	0.64
71_A	75_R	1.488	0.63
132_H	243_S	1.480	0.63
222_K	233_D	1.479	0.63
10_V	175_F	1.474	0.63
11_S	150_T	1.474	0.63
197_P	205_V	1.470	0.62
85_K	150_T	1.466	0.62
81_C	188_G	1.452	0.62
38_C	57_F	1.450	0.61
237_L	242_F	1.443	0.61
157_N	162_Y	1.433	0.60
108_D	239_F	1.425	0.60
82_W	172_C	1.417	0.60
12_R	40_D	1.409	0.59
108_D	149_N	1.407	0.59
212_N	243_S	1.376	0.57
82_W	241_H	1.364	0.57
78_H	149_N	1.363	0.56
127_L	200_F	1.357	0.56
114_D	236_P	1.353	0.56
89_L	165_V	1.338	0.55
75_R	192_Y	1.335	0.55
22_I	34_L	1.331	0.55
209_I	234_E	1.325	0.54
210_G	237_L	1.319	0.54
149_N	241_H	1.314	0.54
68_L	227_D	1.296	0.53
75_R	83_T	1.294	0.53
49_H	227_D	1.288	0.52
149_N	239_F	1.280	0.52
41_Q	61_H	1.280	0.52
130_T	212_N	1.274	0.51
8_T	40_D	1.268	0.51
14_H	132_H	1.268	0.51
122_N	128_Y	1.262	0.51
14_H	241_H	1.257	0.50
49_H	53_E	1.247	0.50
132_H	239_F	1.236	0.49
6_F	32_F	1.224	0.48
9_I	75_R	1.223	0.48
116_A	120_A	1.221	0.48
106_D	216_W	1.221	0.48
6_F	29_C	1.218	0.48
14_H	214_A	1.207	0.47
96_W	234_E	1.201	0.47
159_K	163_E	1.200	0.47
11_S	85_K	1.200	0.47
82_W	108_D	1.200	0.47
127_L	164_A	1.200	0.47
129_L	179_E	1.195	0.47
226_K	229_R	1.191	0.47
33_H	97_D	1.181	0.46
82_W	149_N	1.181	0.46
20_P	111_F	1.180	0.46
149_N	243_S	1.177	0.46
63_M	84_L	1.163	0.45
104_H	167_Q	1.158	0.45
6_F	25_L	1.157	0.45
95_K	163_E	1.151	0.44
250_E	254_N	1.149	0.44
126_S	202_G	1.149	0.44
108_D	132_H	1.147	0.44
167_Q	200_F	1.132	0.43
132_H	150_T	1.131	0.43
117_R	173_I	1.129	0.43
107_T	188_G	1.113	0.42
6_F	155_A	1.093	0.41
158_T	161_A	1.092	0.41
228_G	232_I	1.080	0.40
102_F	152_F	1.073	0.40
226_K	231_Y	1.070	0.40
166_W	170_Q	1.070	0.40
146_G	274_Y	1.062	0.39
240_Y	253_F	1.057	0.39
93_M	162_Y	1.056	0.39
106_D	146_G	1.050	0.39
200_F	213_T	1.049	0.38
86_P	168_W	1.048	0.38
93_M	157_N	1.047	0.38
109_L	221_Y	1.041	0.38
109_L	194_E	1.041	0.38
146_G	190_Q	1.039	0.38
108_D	212_N	1.034	0.38
67_E	159_K	1.034	0.38
136_P	139_M	1.025	0.37
63_M	261_I	1.020	0.37
158_T	202_G	1.017	0.37
245_F	275_I	1.016	0.37
96_W	157_N	1.015	0.37
130_T	152_F	1.008	0.36
131_D	186_T	1.002	0.36
145_T	178_V	1.001	0.36
164_A	196_W	0.997	0.36
20_P	208_S	0.996	0.36
106_D	152_F	0.992	0.35
230_V	233_D	0.990	0.35
35_Y	205_V	0.988	0.35
99_A	157_N	0.987	0.35
200_F	203_V	0.984	0.35
39_V	81_C	0.982	0.35
79_E	171_D	0.979	0.35
8_T	21_M	0.978	0.35
14_H	82_W	0.972	0.34
128_Y	152_F	0.972	0.34
171_D	245_F	0.971	0.34
62_E	66_P	0.968	0.34
161_A	196_W	0.966	0.34
224_G	234_E	0.965	0.34
93_M	99_A	0.965	0.34
103_A	150_T	0.961	0.34
9_I	151_G	0.959	0.34
108_D	191_R	0.956	0.33
75_R	142_Y	0.954	0.33
125_A	156_G	0.946	0.33
37_L	89_L	0.946	0.33
60_L	262_E	0.944	0.33
234_E	269_M	0.940	0.33
227_D	280_R	0.940	0.33
166_W	276_L	0.940	0.33
100_E	156_G	0.940	0.33
116_A	157_N	0.939	0.33
78_H	82_W	0.938	0.33
36_V	140_S	0.933	0.32
83_T	176_C	0.933	0.32
108_D	150_T	0.929	0.32
134_N	164_A	0.927	0.32
107_T	186_T	0.923	0.32
122_N	167_Q	0.922	0.32
66_P	208_S	0.919	0.32
89_L	153_V	0.918	0.32
75_R	215_L	0.918	0.32
131_D	147_R	0.909	0.31
217_N	221_Y	0.907	0.31
75_R	291_D	0.900	0.31
228_G	235_T	0.898	0.31
85_K	154_G	0.897	0.30
33_H	148_F	0.895	0.30
154_G	207_K	0.894	0.30
14_H	239_F	0.892	0.30
9_I	212_N	0.892	0.30
105_M	232_I	0.882	0.30
21_M	34_L	0.878	0.30
27_E	67_E	0.877	0.30
84_L	193_V	0.876	0.29
85_K	167_Q	0.871	0.29
9_I	154_G	0.863	0.29
167_Q	189_D	0.863	0.29
83_T	172_C	0.862	0.29
8_T	15_I	0.858	0.29
268_K	272_M	0.858	0.29
9_I	81_C	0.853	0.28
86_P	287_S	0.852	0.28
277_N	280_R	0.852	0.28
63_M	284_E	0.851	0.28
77_F	85_K	0.843	0.28
152_F	243_S	0.842	0.28
52_W	55_V	0.837	0.28
39_V	84_L	0.836	0.28
75_R	155_A	0.835	0.28
91_H	94_S	0.832	0.27
7_S	199_Q	0.831	0.27
85_K	149_N	0.827	0.27
105_M	149_N	0.825	0.27
86_P	107_T	0.823	0.27
26_H	54_H	0.821	0.27
168_W	217_N	0.811	0.26
27_E	33_H	0.810	0.26
93_M	244_G	0.802	0.26
21_M	247_L	0.801	0.26
77_F	84_L	0.800	0.26
108_D	190_Q	0.799	0.26
38_C	192_Y	0.797	0.26
206_V	211_A	0.795	0.26
150_T	188_G	0.795	0.26
146_G	189_D	0.788	0.25
11_S	188_G	0.787	0.25
131_D	221_Y	0.786	0.25
150_T	214_A	0.786	0.25
155_A	161_A	0.785	0.25
89_L	155_A	0.784	0.25
187_Y	194_E	0.782	0.25
17_K	215_L	0.778	0.25
75_R	127_L	0.777	0.25
95_K	222_K	0.773	0.25
29_C	114_D	0.771	0.25
125_A	228_G	0.768	0.25
212_N	241_H	0.764	0.24
122_N	132_H	0.764	0.24
25_L	32_F	0.762	0.24
35_Y	58_V	0.761	0.24
149_N	176_C	0.760	0.24
12_R	43_A	0.757	0.24
18_L	22_I	0.754	0.24
148_F	163_E	0.754	0.24
108_D	216_W	0.752	0.24
112_F	277_N	0.743	0.23
64_E	133_R	0.742	0.23
25_L	240_Y	0.738	0.23
171_D	200_F	0.733	0.23
89_L	93_M	0.732	0.23
87_A	102_F	0.731	0.23
23_H	280_R	0.730	0.23
84_L	150_T	0.728	0.23
71_A	83_T	0.727	0.23
121_E	128_Y	0.726	0.23
149_N	152_F	0.725	0.23
82_W	168_W	0.722	0.23
176_C	190_Q	0.719	0.22
136_P	187_Y	0.717	0.22
101_Y	154_G	0.715	0.22
110_F	277_N	0.715	0.22
186_T	191_R	0.715	0.22
22_I	32_F	0.714	0.22
83_T	192_Y	0.714	0.22
132_H	241_H	0.714	0.22
188_G	193_V	0.713	0.22
166_W	284_E	0.713	0.22
28_H	225_Q	0.712	0.22
34_L	71_A	0.712	0.22
69_L	72_K	0.709	0.22
78_H	150_T	0.705	0.22
154_G	159_K	0.705	0.22
66_P	280_R	0.705	0.22
135_S	220_N	0.703	0.22
106_D	217_N	0.702	0.22
9_I	150_T	0.701	0.22
148_F	228_G	0.701	0.22
58_V	222_K	0.697	0.22
161_A	194_E	0.696	0.22
15_I	278_L	0.690	0.21
79_E	108_D	0.687	0.21
149_N	244_G	0.687	0.21
150_T	172_C	0.686	0.21
201_K	207_K	0.684	0.21
132_H	211_A	0.683	0.21
27_E	92_V	0.681	0.21
95_K	226_K	0.678	0.21
108_D	172_C	0.678	0.21
41_Q	68_L	0.677	0.21
75_R	175_F	0.676	0.21
121_E	204_H	0.664	0.20
6_F	15_I	0.663	0.20
45_E	270_I	0.662	0.20
70_K	280_R	0.661	0.20
191_R	205_V	0.659	0.20
151_G	197_P	0.652	0.20
106_D	239_F	0.652	0.20
82_W	192_Y	0.652	0.20
176_C	187_Y	0.650	0.20
85_K	106_D	0.650	0.20
106_D	214_A	0.647	0.20
163_E	278_L	0.646	0.20
149_N	190_Q	0.646	0.20
15_I	113_S	0.643	0.20
101_Y	127_L	0.643	0.20
77_F	81_C	0.643	0.20
127_L	155_A	0.640	0.19
33_H	99_A	0.639	0.19
14_H	104_H	0.638	0.19
126_S	160_E	0.630	0.19
118_I	128_Y	0.629	0.19
80_Y	291_D	0.628	0.19
9_I	188_G	0.626	0.19
118_I	206_V	0.625	0.19
108_D	152_F	0.623	0.19
13_T	150_T	0.622	0.19
147_R	152_F	0.618	0.19
128_Y	272_M	0.616	0.19
188_G	241_H	0.611	0.18
190_Q	274_Y	0.611	0.18
222_K	277_N	0.611	0.18
129_L	207_K	0.610	0.18
250_E	257_W	0.609	0.18
25_L	34_L	0.607	0.18
223_V	237_L	0.607	0.18
166_W	263_D	0.606	0.18
108_D	243_S	0.605	0.18
69_L	148_F	0.605	0.18
80_Y	115_P	0.605	0.18
215_L	256_C	0.604	0.18
84_L	118_I	0.604	0.18
75_R	176_C	0.603	0.18
10_V	150_T	0.603	0.18
108_D	189_D	0.603	0.18
25_L	176_C	0.603	0.18
71_A	142_Y	0.601	0.18
134_N	240_Y	0.601	0.18
106_D	167_Q	0.599	0.18
130_T	167_Q	0.597	0.18
105_M	245_F	0.595	0.18
127_L	161_A	0.593	0.18
94_S	112_F	0.591	0.18
67_E	205_V	0.590	0.18
127_L	285_I	0.588	0.18
133_R	142_Y	0.588	0.18
8_T	13_T	0.588	0.18
24_S	181_D	0.585	0.17
14_H	187_Y	0.581	0.17
9_I	215_L	0.581	0.17
29_C	115_P	0.579	0.17
60_L	68_L	0.579	0.17
63_M	212_N	0.578	0.17
93_M	180_M	0.576	0.17
192_Y	200_F	0.575	0.17
70_K	227_D	0.575	0.17
100_E	116_A	0.572	0.17
108_D	151_G	0.571	0.17
106_D	176_C	0.569	0.17
119_F	165_V	0.569	0.17
115_P	192_Y	0.569	0.17
42_K	148_F	0.568	0.17
85_K	131_D	0.567	0.17
75_R	80_Y	0.565	0.17
214_A	217_N	0.564	0.17
5_H	12_R	0.564	0.17
54_H	161_A	0.558	0.17
89_L	200_F	0.558	0.17
199_Q	214_A	0.557	0.17
14_H	17_K	0.557	0.17
67_E	163_E	0.555	0.17
106_D	132_H	0.555	0.17
37_L	130_T	0.554	0.16
127_L	192_Y	0.553	0.16
208_S	235_T	0.550	0.16
95_K	276_L	0.549	0.16
104_H	155_A	0.548	0.16
14_H	109_L	0.548	0.16
120_A	225_Q	0.547	0.16
176_C	191_R	0.546	0.16
85_K	129_L	0.545	0.16
272_M	275_I	0.544	0.16
130_T	214_A	0.543	0.16
23_H	27_E	0.543	0.16
108_D	214_A	0.543	0.16
72_K	188_G	0.542	0.16
162_Y	166_W	0.539	0.16
160_E	207_K	0.537	0.16
205_V	214_A	0.537	0.16
109_L	149_N	0.536	0.16
84_L	89_L	0.536	0.16
91_H	95_K	0.536	0.16
151_G	154_G	0.534	0.16
120_A	124_T	0.531	0.16
223_V	235_T	0.531	0.16
9_I	85_K	0.530	0.16
125_A	220_N	0.529	0.16
79_E	216_W	0.528	0.16
134_N	185_K	0.526	0.16
66_P	229_R	0.526	0.16
71_A	86_P	0.526	0.16
124_T	159_K	0.525	0.16
80_Y	192_Y	0.523	0.16
92_V	174_E	0.521	0.15
126_S	161_A	0.519	0.15
42_K	191_R	0.519	0.15
34_L	259_Y	0.519	0.15
27_E	95_K	0.517	0.15
12_R	181_D	0.516	0.15
167_Q	171_D	0.516	0.15
224_G	276_L	0.515	0.15
129_L	211_A	0.512	0.15
130_T	274_Y	0.512	0.15
75_R	133_R	0.510	0.15
162_Y	224_G	0.508	0.15
107_T	193_V	0.506	0.15
11_S	129_L	0.505	0.15
121_E	208_S	0.504	0.15
130_T	189_D	0.500	0.15

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
1g9rA	1	0.8296	99.8	0.814	Contact Map
3tztA	2	0.7299	99.8	0.819	Contact Map
4uegA	4	0.7878	99.7	0.832	Contact Map
1ll2A	2	0.7781	99.6	0.842	Contact Map
3u2uA	2	0.7974	99.6	0.844	Contact Map
2p6wA	1	0.5981	97.5	0.924	Contact Map
3zf8A	2	0.6945	69.8	0.96	Contact Map
4mixA	1	0.7363	46	0.966	Contact Map
3no3A	1	0.3473	21.4	0.971	Contact Map
3bcvA	2	0.5691	20.5	0.971	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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