YDDB - BACSU - GREMLIN Contacts

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YDDB - Uncharacterized protein YddB

UniProt:	O31491	Sequences: MLNKEIGSDKKEESFFRSAFQKLKRIERPEKDKQKVPRDRSKLIAVTLWSCVGSLLFICLLAVLLSINTRSQLNDMKDETNKPTNDDKQKISVTAAENFLSGFINEYMNVKNDQESIEKRMQSLESYMVKQEDNHFEDEERFNVDGLKGDRELKGYSLYNVKEGDKNSLFQYKVTYENLYPVEKEVEKEVKDGKKKKKVKEKVKTNEKYEKQMLLNIPVTNKGDSFAVSAVPYFTQIYDLKGDIAFKGKEETRDEYAGEKKESIESFLQNFFEKYASEKKEEMVYMMKKPEALEGNLLFGEVQSVKIFETKKGFEVFCAVRFKEKENDIPVNEKFSLEITENSGQFYVNKLKHQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	354 (293)
Sequences:	257 (199)
Seq/√Len:	11.6

BACSU - YDDB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
272_F	335_F	3.598	0.98
268_L	272_F	3.552	0.98
320_V	339_I	3.544	0.98
307_I	314_F	3.300	0.97
176_Y	333_E	3.246	0.97
276_A	320_V	3.151	0.96
99_F	241_K	3.126	0.96
285_Y	345_Q	3.032	0.95
27_E	30_E	2.884	0.94
271_F	275_Y	2.873	0.94
278_E	282_E	2.867	0.94
111_K	264_I	2.856	0.94
276_A	322_F	2.781	0.93
274_K	282_E	2.680	0.91
265_E	307_I	2.648	0.91
221_N	224_D	2.607	0.90
287_M	290_P	2.396	0.86
108_M	215_L	2.345	0.84
272_F	299_F	2.320	0.84
308_F	347_Y	2.230	0.81
314_F	339_I	2.221	0.81
109_N	153_L	2.216	0.81
108_M	151_R	2.206	0.81
305_V	320_V	2.170	0.79
100_L	170_F	2.161	0.79
323_K	328_D	2.154	0.79
274_K	287_M	2.142	0.78
172_Y	235_T	2.142	0.78
54_S	307_I	2.107	0.77
170_F	219_V	2.083	0.76
302_V	330_P	2.020	0.74
122_Q	342_N	1.948	0.71
233_Y	274_K	1.936	0.71
26_I	33_K	1.894	0.69
264_I	307_I	1.822	0.66
274_K	333_E	1.789	0.64
73_L	76_M	1.773	0.64
108_M	339_I	1.755	0.63
127_Y	264_I	1.700	0.60
45_A	58_I	1.696	0.60
128_M	244_I	1.695	0.60
233_Y	283_M	1.659	0.58
99_F	285_Y	1.621	0.57
274_K	290_P	1.616	0.56
316_V	337_L	1.604	0.56
272_F	320_V	1.599	0.55
114_Q	118_E	1.591	0.55
119_K	351_L	1.585	0.55
100_L	172_Y	1.584	0.55
30_E	33_K	1.580	0.55
103_F	107_Y	1.567	0.54
104_I	172_Y	1.548	0.53
294_E	349_N	1.530	0.52
280_K	288_K	1.525	0.52
330_P	339_I	1.522	0.52
111_K	237_I	1.513	0.51
301_E	321_R	1.506	0.51
47_T	300_G	1.490	0.50
30_E	34_Q	1.484	0.50
27_E	33_K	1.480	0.50
283_M	337_L	1.476	0.49
110_V	151_R	1.463	0.49
41_S	44_I	1.461	0.49
272_F	322_F	1.456	0.48
58_I	62_A	1.447	0.48
222_K	299_F	1.443	0.48
231_V	234_F	1.434	0.47
322_F	335_F	1.430	0.47
264_I	314_F	1.419	0.47
95_A	335_F	1.416	0.46
97_E	161_V	1.406	0.46
279_K	300_G	1.401	0.46
156_Y	320_V	1.379	0.45
109_N	124_L	1.374	0.44
48_L	66_S	1.366	0.44
110_V	346_F	1.357	0.44
233_Y	287_M	1.356	0.43
282_E	290_P	1.354	0.43
161_V	318_C	1.329	0.42
133_D	351_L	1.327	0.42
82_K	173_K	1.324	0.42
245_A	269_Q	1.320	0.42
28_R	31_K	1.311	0.41
110_V	120_R	1.285	0.40
308_F	343_S	1.275	0.40
98_N	285_Y	1.273	0.40
27_E	31_K	1.270	0.39
262_E	329_I	1.262	0.39
216_N	283_M	1.262	0.39
108_M	331_V	1.259	0.39
45_A	238_Y	1.249	0.38
122_Q	175_T	1.247	0.38
159_Y	285_Y	1.244	0.38
270_N	285_Y	1.229	0.37
268_L	299_F	1.222	0.37
251_E	257_A	1.218	0.37
223_G	299_F	1.210	0.37
107_Y	320_V	1.199	0.36
100_L	104_I	1.187	0.36
25_R	30_E	1.182	0.35
274_K	283_M	1.179	0.35
158_L	172_Y	1.176	0.35
153_L	156_Y	1.176	0.35
128_M	333_E	1.172	0.35
26_I	153_L	1.171	0.35
108_M	139_E	1.165	0.35
217_I	289_K	1.163	0.34
158_L	283_M	1.158	0.34
172_Y	176_Y	1.153	0.34
226_F	316_V	1.145	0.34
170_F	282_E	1.145	0.34
57_F	62_A	1.129	0.33
91_I	109_N	1.126	0.33
120_R	316_V	1.123	0.33
322_F	333_E	1.120	0.33
134_N	217_I	1.120	0.33
281_E	293_L	1.118	0.32
278_E	281_E	1.117	0.32
25_R	28_R	1.114	0.32
288_K	347_Y	1.112	0.32
176_Y	322_F	1.109	0.32
180_Y	318_C	1.109	0.32
57_F	162_K	1.108	0.32
106_E	235_T	1.107	0.32
126_S	177_E	1.104	0.32
104_I	123_S	1.095	0.31
40_R	43_L	1.082	0.31
48_L	52_V	1.077	0.31
215_L	348_V	1.076	0.31
60_L	279_K	1.074	0.31
48_L	150_D	1.073	0.31
151_R	176_Y	1.063	0.30
38_R	179_L	1.063	0.30
295_G	324_E	1.063	0.30
162_K	260_K	1.052	0.30
56_L	217_I	1.050	0.30
272_F	275_Y	1.048	0.30
151_R	287_M	1.047	0.29
66_S	99_F	1.042	0.29
108_M	287_M	1.039	0.29
271_F	348_V	1.037	0.29
174_V	305_V	1.036	0.29
151_R	171_Q	1.033	0.29
266_S	269_Q	1.031	0.29
54_S	346_F	1.024	0.29
150_D	328_D	1.024	0.29
151_R	290_P	1.023	0.28
304_S	319_A	1.020	0.28
321_R	330_P	1.014	0.28
122_Q	312_K	1.009	0.28
92_S	345_Q	1.005	0.28
92_S	228_V	1.004	0.28
38_R	42_K	1.004	0.28
268_L	302_V	1.000	0.28
104_I	160_N	0.998	0.27
270_N	333_E	0.994	0.27
267_F	283_M	0.991	0.27
176_Y	267_F	0.991	0.27
82_K	312_K	0.990	0.27
215_L	308_F	0.986	0.27
133_D	348_V	0.985	0.27
214_L	235_T	0.976	0.27
64_L	99_F	0.972	0.26
45_A	102_G	0.960	0.26
146_G	330_P	0.955	0.26
100_L	297_L	0.955	0.26
122_Q	269_Q	0.948	0.26
259_E	343_S	0.945	0.25
107_Y	232_P	0.942	0.25
239_D	343_S	0.940	0.25
159_Y	238_Y	0.933	0.25
285_Y	324_E	0.931	0.25
101_S	111_K	0.929	0.25
54_S	125_E	0.926	0.25
59_C	64_L	0.923	0.25
78_D	99_F	0.922	0.25
148_K	346_F	0.921	0.25
171_Q	215_L	0.919	0.24
98_N	278_E	0.918	0.24
114_Q	313_G	0.918	0.24
309_E	341_E	0.918	0.24
172_Y	182_V	0.917	0.24
98_N	241_K	0.917	0.24
233_Y	290_P	0.915	0.24
182_V	207_E	0.912	0.24
65_L	335_F	0.910	0.24
179_L	252_T	0.908	0.24
277_S	294_E	0.907	0.24
234_F	331_V	0.892	0.24
155_G	217_I	0.888	0.23
111_K	132_E	0.885	0.23
34_Q	54_S	0.879	0.23
55_L	251_E	0.869	0.23
183_E	312_K	0.866	0.23
61_L	300_G	0.862	0.22
281_E	347_Y	0.858	0.22
100_L	219_V	0.858	0.22
124_L	262_E	0.857	0.22
36_V	215_L	0.852	0.22
108_M	231_V	0.851	0.22
169_L	219_V	0.847	0.22
295_G	313_G	0.842	0.22
172_Y	333_E	0.836	0.22
123_S	126_S	0.833	0.21
46_V	113_D	0.833	0.21
238_Y	345_Q	0.832	0.21
49_W	285_Y	0.831	0.21
60_L	318_C	0.830	0.21
45_A	285_Y	0.829	0.21
222_K	229_S	0.826	0.21
120_R	124_L	0.825	0.21
72_Q	262_E	0.823	0.21
127_Y	278_E	0.822	0.21
241_K	298_L	0.819	0.21
23_L	27_E	0.818	0.21
303_Q	321_R	0.816	0.21
67_I	110_V	0.811	0.21
42_K	46_V	0.808	0.21
44_I	347_Y	0.807	0.21
267_F	282_E	0.805	0.21
129_V	228_V	0.805	0.21
95_A	272_F	0.804	0.21
224_D	311_K	0.798	0.20
106_E	111_K	0.797	0.20
161_V	302_V	0.796	0.20
268_L	283_M	0.796	0.20
270_N	282_E	0.793	0.20
53_G	236_Q	0.786	0.20
63_V	113_D	0.785	0.20
161_V	320_V	0.784	0.20
229_S	304_S	0.776	0.20
55_L	149_G	0.774	0.20
100_L	335_F	0.773	0.20
348_V	351_L	0.773	0.20
340_T	349_N	0.769	0.19
328_D	348_V	0.767	0.19
37_P	40_R	0.766	0.19
37_P	110_V	0.766	0.19
260_K	289_K	0.765	0.19
56_L	94_T	0.765	0.19
270_N	283_M	0.764	0.19
47_T	114_Q	0.763	0.19
59_C	100_L	0.762	0.19
181_P	292_A	0.762	0.19
300_G	323_K	0.757	0.19
47_T	297_L	0.753	0.19
268_L	322_F	0.751	0.19
56_L	302_V	0.749	0.19
109_N	281_E	0.748	0.19
67_I	346_F	0.747	0.19
159_Y	276_A	0.746	0.19
182_V	228_V	0.743	0.19
273_E	336_S	0.742	0.19
56_L	104_I	0.742	0.19
100_L	331_V	0.742	0.19
154_K	177_E	0.741	0.19
124_L	155_G	0.740	0.19
263_S	341_E	0.733	0.18
66_S	149_G	0.731	0.18
339_I	344_G	0.730	0.18
70_R	76_M	0.727	0.18
233_Y	333_E	0.727	0.18
163_E	234_F	0.726	0.18
53_G	259_E	0.723	0.18
113_D	208_K	0.723	0.18
170_F	299_F	0.721	0.18
91_I	154_K	0.721	0.18
96_A	99_F	0.720	0.18
55_L	238_Y	0.719	0.18
230_A	286_M	0.719	0.18
35_K	73_L	0.719	0.18
129_V	227_A	0.712	0.18
151_R	335_F	0.712	0.18
265_E	305_V	0.709	0.18
108_M	276_A	0.709	0.18
43_L	174_V	0.709	0.18
82_K	116_S	0.705	0.18
82_K	257_A	0.704	0.17
111_K	243_D	0.703	0.17
49_W	307_I	0.702	0.17
125_E	149_G	0.699	0.17
282_E	333_E	0.692	0.17
55_L	283_M	0.690	0.17
48_L	62_A	0.689	0.17
62_A	66_S	0.689	0.17
122_Q	262_E	0.689	0.17
62_A	272_F	0.686	0.17
48_L	339_I	0.682	0.17
99_F	226_F	0.682	0.17
171_Q	214_L	0.675	0.17
60_L	339_I	0.675	0.17
231_V	323_K	0.672	0.17
269_Q	309_E	0.671	0.17
164_G	174_V	0.670	0.17
310_T	340_T	0.668	0.16
82_K	297_L	0.667	0.16
342_N	347_Y	0.667	0.16
122_Q	246_F	0.666	0.16
42_K	234_F	0.666	0.16
102_G	239_D	0.665	0.16
94_T	121_M	0.665	0.16
151_R	286_M	0.665	0.16
108_M	283_M	0.662	0.16
74_N	93_V	0.660	0.16
233_Y	282_E	0.659	0.16
246_F	302_V	0.659	0.16
333_E	336_S	0.659	0.16
158_L	286_M	0.654	0.16
221_N	282_E	0.653	0.16
151_R	234_F	0.652	0.16
100_L	333_E	0.651	0.16
109_N	157_S	0.650	0.16
36_V	236_Q	0.649	0.16
278_E	295_G	0.648	0.16
155_G	230_A	0.647	0.16
60_L	302_V	0.646	0.16
119_K	217_I	0.646	0.16
37_P	228_V	0.645	0.16
212_Q	322_F	0.644	0.16
119_K	169_L	0.644	0.16
314_F	330_P	0.641	0.16
100_L	217_I	0.639	0.16
103_F	131_Q	0.639	0.16
92_S	288_K	0.638	0.16
150_D	327_N	0.638	0.16
120_R	320_V	0.637	0.16
80_T	156_Y	0.637	0.16
122_Q	163_E	0.636	0.16
166_K	207_E	0.635	0.16
119_K	212_Q	0.634	0.16
118_E	208_K	0.631	0.16
89_Q	157_S	0.629	0.15
69_T	73_L	0.629	0.15
304_S	316_V	0.628	0.15
63_V	73_L	0.627	0.15
287_M	333_E	0.626	0.15
168_S	228_V	0.626	0.15
23_L	30_E	0.623	0.15
171_Q	265_E	0.622	0.15
153_L	233_Y	0.619	0.15
25_R	40_R	0.618	0.15
127_Y	305_V	0.618	0.15
224_D	294_E	0.614	0.15
49_W	219_V	0.612	0.15
90_K	113_D	0.612	0.15
114_Q	335_F	0.611	0.15
302_V	316_V	0.611	0.15
49_W	94_T	0.610	0.15
120_R	267_F	0.610	0.15
304_S	346_F	0.609	0.15
42_K	64_L	0.607	0.15
124_L	315_E	0.606	0.15
34_Q	89_Q	0.602	0.15
221_N	226_F	0.598	0.15
259_E	269_Q	0.597	0.15
176_Y	286_M	0.597	0.15
152_E	291_E	0.597	0.15
75_D	159_Y	0.596	0.15
112_N	117_I	0.593	0.15
183_E	256_Y	0.592	0.15
122_Q	125_E	0.591	0.15
320_V	348_V	0.591	0.15
104_I	226_F	0.590	0.14
23_L	34_Q	0.590	0.14
103_F	232_P	0.587	0.14
101_S	156_Y	0.586	0.14
122_Q	165_D	0.584	0.14
243_D	350_K	0.583	0.14
70_R	110_V	0.583	0.14
151_R	278_E	0.582	0.14
127_Y	315_E	0.580	0.14
162_K	261_K	0.579	0.14
97_E	339_I	0.578	0.14
89_Q	248_G	0.578	0.14
217_I	227_A	0.575	0.14
124_L	271_F	0.575	0.14
127_Y	220_T	0.575	0.14
288_K	301_E	0.570	0.14
172_Y	347_Y	0.569	0.14
63_V	152_E	0.567	0.14
50_S	349_N	0.567	0.14
206_N	337_L	0.567	0.14
151_R	214_L	0.565	0.14
66_S	110_V	0.565	0.14
108_M	159_Y	0.564	0.14
46_V	228_V	0.564	0.14
219_V	331_V	0.563	0.14
263_S	320_V	0.563	0.14
216_N	343_S	0.562	0.14
99_F	107_Y	0.560	0.14
177_E	288_K	0.560	0.14
58_I	69_T	0.558	0.14
41_S	178_N	0.558	0.14
209_Y	248_G	0.557	0.14
172_Y	267_F	0.557	0.14
181_P	257_A	0.557	0.14
169_L	289_K	0.556	0.14
106_E	123_S	0.554	0.14
162_K	236_Q	0.550	0.14
233_Y	348_V	0.549	0.14
99_F	266_S	0.549	0.14
182_V	298_L	0.547	0.13
75_D	256_Y	0.546	0.13
285_Y	347_Y	0.546	0.13
96_A	129_V	0.545	0.13
96_A	316_V	0.544	0.13
116_S	303_Q	0.543	0.13
61_L	81_N	0.542	0.13
273_E	351_L	0.540	0.13
112_N	150_D	0.537	0.13
107_Y	158_L	0.537	0.13
131_Q	265_E	0.536	0.13
182_V	311_K	0.535	0.13
122_Q	309_E	0.534	0.13
313_G	339_I	0.530	0.13
241_K	342_N	0.528	0.13
146_G	178_N	0.526	0.13
47_T	206_N	0.525	0.13
302_V	339_I	0.522	0.13
35_K	350_K	0.522	0.13
228_V	239_D	0.521	0.13
58_I	61_L	0.521	0.13
33_K	121_M	0.520	0.13
98_N	237_I	0.520	0.13
234_F	333_E	0.520	0.13
175_T	324_E	0.518	0.13
35_K	266_S	0.518	0.13
66_S	333_E	0.514	0.13
158_L	227_A	0.511	0.13
164_G	227_A	0.508	0.13
45_A	335_F	0.507	0.13
280_K	309_E	0.505	0.13
115_E	312_K	0.504	0.12
34_Q	247_K	0.503	0.12
58_I	67_I	0.503	0.12
329_I	346_F	0.502	0.12
142_F	146_G	0.501	0.12
154_K	237_I	0.501	0.12
163_E	248_G	0.500	0.12
124_L	336_S	0.500	0.12

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
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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
3ub1A	3	0.6667	100	0.487	Contact Map
4ec6A	3	0.3079	99.6	0.792	Contact Map
3k7cA	2	0.2401	75	0.947	Contact Map
1vqqA	1	0.2486	46.4	0.956	Contact Map
3kztA	2	0.2938	42.1	0.957	Contact Map
3b7cA	2	0.2599	39.9	0.957	Contact Map
3bb9A	2	0.2768	39.7	0.957	Contact Map
3f7sA	2	0.2797	35.5	0.958	Contact Map
4ovmA	2	0.2712	19	0.964	Contact Map
2rgqA	3	0.2853	16.8	0.965	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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