YBDG - BACSU - GREMLIN Contacts

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YBDG - Uncharacterized protein YbdG

UniProt:	O31431	Sequences: MKTLWKVLKIVFVSLAALVLLVSVSVFIYHHFQLNKEAALLKGKGTVVDVDGKKMNVYQEGSGKDTFVFMSGSGIAAPAYEMKGLYSKFSKENKIAVVDRAGYGYSEVSHDDRDIDTVLEQTRKALMKSGNKPPYILMPHSISGIEAMYWAQKYPKEIKAIIAMDIGLPQQYVTYKLSGVDRLKVRGFHLLTSIGFHRFIPSAVYNPEVIRQSFLTDEEKEIYKAINFKQFFNADMEHELLQSYQNGSKSVNLPAPKETPVLILDAVSDQNRHSKYAIQNRKDYEAFAAQFNTADIKELRGTHSIYLYQPDQIYKLSMEFMRKVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (261)
Sequences:	49247 (39683)
Seq/√Len:	2456.3

ECOLI - MHPC RUTD BIOH YBFF PLDB MENH YFHR YCJY
BACSU - YBDG YUGF YRAK NAP MENH YFHM YCGS YBFK YDJP YISY RSBQ YBAC YQJL YVAM YCLE PLBAC EST YQKD
HALSA - Q9HHP4 Q9HRJ0 Q9HPT9
SULSO - PIP Q97WG0 Q7LXY9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_Q	94_K	5.100	1.00
136_I	160_A	4.405	1.00
101_A	121_Q	4.161	1.00
85_L	314_Y	3.243	1.00
309_Q	312_Q	2.923	1.00
123_R	150_W	2.882	1.00
136_I	159_K	2.708	1.00
92_E	318_M	2.616	1.00
165_D	269_D	2.522	1.00
134_P	159_K	2.504	1.00
54_K	107_E	2.485	1.00
262_L	320_F	2.425	1.00
164_M	313_I	2.381	1.00
58_Y	77_A	2.335	1.00
297_K	316_L	2.321	1.00
299_L	316_L	2.310	1.00
126_L	135_Y	2.258	1.00
150_W	154_Y	2.197	1.00
123_R	157_E	2.167	1.00
123_R	127_M	2.130	1.00
49_D	54_K	2.129	1.00
123_R	154_Y	2.112	1.00
127_M	157_E	2.110	1.00
144_G	166_I	2.091	1.00
56_N	105_Y	2.058	1.00
137_L	147_A	1.998	1.00
120_E	153_K	1.947	1.00
57_V	125_A	1.928	1.00
301_G	309_Q	1.875	1.00
59_Q	96_A	1.842	1.00
288_A	294_A	1.836	1.00
47_V	54_K	1.829	1.00
149_Y	153_K	1.815	1.00
136_I	321_M	1.812	1.00
88_K	314_Y	1.776	1.00
56_N	77_A	1.761	1.00
60_E	97_V	1.753	1.00
136_I	162_I	1.735	1.00
71_S	103_Y	1.708	1.00
151_A	161_I	1.704	1.00
147_A	161_I	1.677	1.00
316_L	319_E	1.676	1.00
66_T	131_N	1.658	1.00
98_V	122_T	1.656	1.00
93_N	136_I	1.648	1.00
315_K	319_E	1.613	1.00
66_T	96_A	1.604	1.00
116_D	153_K	1.599	1.00
267_V	298_E	1.594	1.00
71_S	100_R	1.593	1.00
100_R	146_E	1.555	1.00
61_G	94_K	1.552	1.00
114_D	117_T	1.538	1.00
261_V	291_F	1.514	1.00
66_T	94_K	1.508	1.00
51_D	124_K	1.503	1.00
286_A	290_Q	1.484	1.00
274_S	298_E	1.466	1.00
122_T	150_W	1.459	1.00
70_M	122_T	1.454	1.00
162_I	317_S	1.441	1.00
150_W	158_I	1.435	1.00
70_M	100_R	1.430	1.00
154_Y	157_E	1.424	1.00
262_L	297_K	1.405	1.00
75_I	81_E	1.402	1.00
119_L	149_Y	1.402	1.00
76_A	80_Y	1.393	1.00
70_M	147_A	1.393	1.00
46_T	57_V	1.385	1.00
56_N	99_D	1.352	1.00
60_E	86_Y	1.337	1.00
55_M	121_Q	1.335	1.00
74_G	103_Y	1.334	1.00
312_Q	316_L	1.317	1.00
88_K	318_M	1.316	1.00
96_A	125_A	1.315	1.00
253_L	256_P	1.307	1.00
291_F	294_A	1.295	1.00
69_F	138_M	1.291	1.00
99_D	104_G	1.283	1.00
150_W	157_E	1.279	1.00
86_Y	97_V	1.276	1.00
68_V	126_L	1.274	1.00
163_A	166_I	1.274	1.00
69_F	95_I	1.252	1.00
53_K	101_A	1.240	1.00
92_E	322_R	1.228	1.00
216_T	219_E	1.226	1.00
141_S	303_H	1.219	1.00
46_T	50_V	1.218	1.00
88_K	91_K	1.212	1.00
148_M	163_A	1.206	1.00
312_Q	315_K	1.205	1.00
98_V	125_A	1.187	1.00
149_Y	152_Q	1.186	1.00
162_I	262_L	1.181	1.00
77_A	105_Y	1.168	1.00
138_M	164_M	1.160	1.00
77_A	99_D	1.147	1.00
140_H	306_Y	1.145	1.00
265_D	284_Y	1.144	1.00
255_A	290_Q	1.138	1.00
285_E	289_A	1.128	1.00
240_L	243_S	1.114	1.00
67_F	93_N	1.109	1.00
88_K	311_D	1.100	1.00
131_N	134_P	1.096	1.00
126_L	131_N	1.089	1.00
241_L	244_Y	1.087	1.00
127_M	154_Y	1.082	1.00
131_N	135_Y	1.080	1.00
313_I	317_S	1.077	1.00
65_D	136_I	1.077	1.00
60_E	90_S	1.071	1.00
72_G	141_S	1.067	1.00
126_L	150_W	1.067	1.00
74_G	141_S	1.061	1.00
267_V	300_R	1.059	1.00
240_L	244_Y	1.055	1.00
125_A	129_S	1.054	1.00
55_M	106_S	1.038	1.00
66_T	93_N	1.028	1.00
46_T	59_Q	1.028	1.00
185_V	189_H	1.027	1.00
70_M	137_L	1.026	1.00
47_V	56_N	1.026	1.00
274_S	285_E	1.020	1.00
64_K	94_K	1.017	1.00
67_F	95_I	1.015	1.00
311_D	315_K	1.014	1.00
57_V	129_S	1.013	1.00
138_M	317_S	1.009	1.00
90_S	95_I	1.007	1.00
65_D	159_K	1.005	1.00
286_A	289_A	1.004	1.00
77_A	80_Y	1.004	1.00
265_D	274_S	1.002	1.00
140_H	304_S	0.998	1.00
264_L	299_L	0.991	1.00
301_G	305_I	0.988	1.00
77_A	97_V	0.983	1.00
221_E	225_A	0.983	1.00
93_N	321_M	0.977	1.00
264_L	316_L	0.975	1.00
254_P	257_K	0.972	1.00
124_K	128_K	0.966	1.00
135_Y	158_I	0.964	1.00
47_V	50_V	0.948	1.00
119_L	146_E	0.945	1.00
116_D	149_Y	0.944	1.00
48_V	57_V	0.943	1.00
53_K	107_E	0.942	1.00
123_R	126_L	0.939	1.00
295_D	316_L	0.939	1.00
96_A	129_S	0.938	1.00
68_V	122_T	0.922	1.00
198_R	201_P	0.915	1.00
83_K	97_V	0.914	1.00
197_H	201_P	0.912	1.00
84_G	87_S	0.910	1.00
68_V	135_Y	0.905	1.00
50_V	124_K	0.900	1.00
234_A	238_H	0.899	1.00
299_L	312_Q	0.892	1.00
152_Q	253_L	0.889	1.00
117_T	120_E	0.887	1.00
301_G	308_Y	0.884	1.00
70_M	98_V	0.882	1.00
318_M	322_R	0.881	1.00
139_P	147_A	0.880	1.00
268_S	300_R	0.878	1.00
135_Y	157_E	0.878	1.00
187_G	191_L	0.876	1.00
217_D	221_E	0.873	1.00
285_E	288_A	0.871	1.00
123_R	153_K	0.866	1.00
199_F	203_A	0.857	1.00
87_S	90_S	0.852	1.00
86_Y	95_I	0.851	1.00
124_K	127_M	0.851	1.00
302_T	308_Y	0.845	1.00
262_L	295_D	0.832	1.00
160_A	260_P	0.830	1.00
151_A	158_I	0.828	1.00
161_I	261_V	0.827	1.00
112_D	117_T	0.827	1.00
266_A	305_I	0.824	1.00
297_K	319_E	0.816	1.00
48_V	128_K	0.800	1.00
58_Y	83_K	0.796	1.00
300_R	309_Q	0.792	1.00
119_L	153_K	0.790	1.00
55_M	101_A	0.789	1.00
137_L	150_W	0.788	1.00
56_N	106_S	0.787	1.00
139_P	144_G	0.785	1.00
165_D	265_D	0.784	1.00
265_D	296_I	0.782	1.00
188_F	192_T	0.782	1.00
69_F	82_M	0.780	1.00
120_E	123_R	0.780	1.00
186_R	189_H	0.774	1.00
258_E	292_N	0.762	1.00
65_D	93_N	0.759	1.00
99_D	105_Y	0.758	1.00
120_E	124_K	0.757	1.00
67_F	138_M	0.756	1.00
184_K	187_G	0.754	1.00
164_M	306_Y	0.752	1.00
100_R	142_I	0.750	1.00
118_V	142_I	0.749	1.00
249_K	252_N	0.749	1.00
140_H	165_D	0.747	1.00
225_A	229_K	0.747	1.00
164_M	305_I	0.746	1.00
77_A	98_V	0.737	1.00
222_I	225_A	0.733	1.00
149_Y	253_L	0.732	1.00
100_R	118_V	0.732	1.00
237_E	240_L	0.729	1.00
81_E	306_Y	0.728	1.00
265_D	298_E	0.727	1.00
191_L	194_I	0.727	1.00
160_A	320_F	0.726	1.00
130_G	134_P	0.726	1.00
285_E	298_E	0.725	1.00
91_K	318_M	0.717	1.00
87_S	91_K	0.717	1.00
221_E	224_K	0.716	1.00
263_I	294_A	0.714	1.00
65_D	134_P	0.713	1.00
226_I	229_K	0.710	1.00
165_D	305_I	0.707	1.00
60_E	87_S	0.707	1.00
158_I	259_T	0.707	1.00
297_K	312_Q	0.707	1.00
139_P	143_S	0.707	1.00
314_Y	318_M	0.704	1.00
162_I	321_M	0.704	1.00
257_K	261_V	0.703	1.00
236_M	240_L	0.703	1.00
264_L	313_I	0.702	1.00
219_E	222_I	0.702	1.00
201_P	204_V	0.701	1.00
226_I	230_Q	0.699	1.00
137_L	158_I	0.699	1.00
246_N	249_K	0.699	1.00
74_G	142_I	0.698	1.00
66_T	135_Y	0.698	1.00
93_N	318_M	0.697	1.00
299_L	309_Q	0.695	1.00
183_L	186_R	0.694	1.00
211_R	214_F	0.694	1.00
71_S	98_V	0.692	1.00
94_K	131_N	0.691	1.00
62_S	94_K	0.690	1.00
239_E	242_Q	0.690	1.00
119_L	150_W	0.688	1.00
212_Q	215_L	0.686	1.00
50_V	53_K	0.686	1.00
195_G	198_R	0.685	1.00
183_L	187_G	0.680	1.00
209_V	212_Q	0.679	1.00
267_V	274_S	0.674	1.00
238_H	242_Q	0.674	1.00
189_H	193_S	0.672	1.00
242_Q	245_Q	0.672	1.00
218_E	222_I	0.669	1.00
135_Y	159_K	0.666	1.00
63_G	94_K	0.662	1.00
88_K	92_E	0.659	1.00
63_G	66_T	0.656	1.00
93_N	322_R	0.655	1.00
284_Y	288_A	0.654	1.00
269_D	303_H	0.653	1.00
68_V	137_L	0.647	1.00
218_E	221_E	0.640	1.00
160_A	321_M	0.640	1.00
144_G	163_A	0.639	1.00
116_D	120_E	0.637	1.00
101_A	118_V	0.634	1.00
69_F	97_V	0.634	1.00
190_L	194_I	0.633	1.00
236_M	239_E	0.631	1.00
222_I	226_I	0.628	1.00
202_S	205_Y	0.626	1.00
85_L	313_I	0.625	1.00
118_V	146_E	0.625	1.00
238_H	241_L	0.624	1.00
162_I	264_L	0.621	1.00
288_A	296_I	0.620	1.00
263_I	291_F	0.619	1.00
151_A	259_T	0.618	1.00
237_E	241_L	0.617	1.00
188_F	191_L	0.616	1.00
73_S	142_I	0.615	1.00
275_K	285_E	0.613	1.00
203_A	206_N	0.612	1.00
184_K	188_F	0.611	1.00
100_R	103_Y	0.610	1.00
187_G	190_L	0.610	1.00
140_H	164_M	0.609	1.00
227_N	231_F	0.608	1.00
67_F	136_I	0.607	1.00
284_Y	296_I	0.604	1.00
85_L	88_K	0.604	1.00
198_R	202_S	0.601	1.00
190_L	193_S	0.601	1.00
120_E	154_Y	0.598	1.00
138_M	162_I	0.598	1.00
184_K	191_L	0.598	1.00
100_R	122_T	0.597	1.00
148_M	166_I	0.595	1.00
68_V	98_V	0.591	1.00
83_K	87_S	0.589	1.00
51_D	120_E	0.588	1.00
310_P	314_Y	0.587	1.00
285_E	296_I	0.587	1.00
184_K	194_I	0.584	1.00
185_V	188_F	0.584	1.00
315_K	318_M	0.583	1.00
70_M	146_E	0.582	1.00
283_D	286_A	0.581	1.00
212_Q	216_T	0.578	1.00
132_K	157_E	0.578	1.00
268_S	301_G	0.577	1.00
96_A	131_N	0.576	1.00
47_V	57_V	0.575	1.00
151_A	257_K	0.575	1.00
196_F	204_V	0.573	1.00
102_G	113_R	0.572	1.00
51_D	117_T	0.571	1.00
126_L	157_E	0.570	1.00
186_R	191_L	0.569	1.00
82_M	85_L	0.566	1.00
241_L	245_Q	0.565	1.00
200_I	203_A	0.562	1.00
115_I	149_Y	0.562	1.00
224_K	228_F	0.561	1.00
319_E	322_R	0.559	1.00
196_F	203_A	0.559	1.00
235_D	238_H	0.558	1.00
162_I	320_F	0.558	1.00
263_I	284_Y	0.557	1.00
67_F	89_F	0.556	1.00
257_K	291_F	0.556	1.00
145_I	167_G	0.555	1.00
267_V	299_L	0.555	1.00
233_N	236_M	0.554	1.00
142_I	146_E	0.554	1.00
141_S	304_S	0.553	1.00
67_F	321_M	0.552	1.00
223_Y	226_I	0.552	1.00
195_G	203_A	0.549	1.00
191_L	195_G	0.549	1.00
72_G	140_H	0.546	1.00
233_N	237_E	0.545	1.00
80_Y	83_K	0.544	1.00
148_M	168_L	0.544	1.00
225_A	228_F	0.542	1.00
295_D	319_E	0.542	1.00
186_R	190_L	0.541	1.00
239_E	243_S	0.539	1.00
200_I	204_V	0.537	1.00
86_Y	90_S	0.535	1.00
152_Q	256_P	0.533	1.00
65_D	160_A	0.533	1.00
201_P	205_Y	0.531	1.00
296_I	299_L	0.527	1.00
84_G	219_E	0.525	1.00
59_Q	129_S	0.524	1.00
265_D	272_R	0.522	1.00
82_M	86_Y	0.519	1.00
235_D	239_E	0.518	1.00
247_G	250_S	0.513	1.00
263_I	288_A	0.513	1.00
135_Y	150_W	0.513	1.00
49_D	52_G	0.510	1.00
197_H	204_V	0.509	1.00
140_H	305_I	0.508	1.00
101_A	109_S	0.507	1.00
73_S	103_Y	0.506	1.00
134_P	157_E	0.506	1.00
314_Y	319_E	0.505	1.00
306_Y	313_I	0.505	1.00
184_K	192_T	0.505	1.00
75_I	304_S	0.503	1.00
119_L	123_R	0.502	1.00
195_G	202_S	0.501	1.00
220_K	224_K	0.500	1.00
197_H	202_S	0.500	1.00

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
4inzA	1	0.8185	100	0.253	Contact Map
3om8A	4	0.8123	100	0.257	Contact Map
1ehyA	1	0.8062	100	0.266	Contact Map
2xuaA	2	0.7938	100	0.274	Contact Map
3oosA	1	0.8062	100	0.276	Contact Map
3r40A	2	0.8369	100	0.279	Contact Map
4ns4A	1	0.8123	100	0.281	Contact Map
2pujA	4	0.8277	100	0.282	Contact Map
4psuA	1	0.8431	100	0.286	Contact Map
2wueA	4	0.8277	100	0.29	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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