YTMO - BACSU - GREMLIN Contacts

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YTMO - Uncharacterized protein YtmO

UniProt:	O34846	Sequences: MIRLSILDQSLIGEGETAADTLQHTVKLAQMAEECGYHRFWVAEHHNNDEIAGSAPEVLLGYLAASTRKIRLASGGVMLQHYSSYKVAEQFHLLSALAPGRIDLGVGKAPGGFQLSTDALQAEYKKPVRQFDEKLEELTHFVRDDFPDTHRYAALRPRPQVDRKPGIFLLGGSTESAISAAKLGISFVFAYFINGEEEVLKEARRAFDAHLPPGSEAEFHLAPAVFAAHTKEEAEKHIVSRESIKVVLKDGRKVNVGSREQAEAYLENVTEPYDIIVQKTGIIAGTKEEVAEELTRLSGTYKINDFVIFTPIKNAVEKQLSYQLLSDAVLAAKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	334 (296)
Sequences:	16569 (10632)
Seq/√Len:	618.0

ECOLI - YHBW RUTA SSUD
BACSU - YTMO YWCH YDDN YCEB YVBT SSUD YXEK MOXC
HALSA - Q9HQZ9
SULSO - Q97Y17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
231_K	289_E	5.415	1.00
30_Q	66_S	3.463	1.00
31_M	323_Q	2.997	1.00
231_K	286_T	2.844	1.00
132_D	182_K	2.793	1.00
71_R	103_D	2.788	1.00
31_M	34_E	2.706	1.00
293_E	296_R	2.673	1.00
33_E	69_K	2.661	1.00
201_K	205_R	2.491	1.00
178_I	206_A	2.459	1.00
230_T	233_E	2.450	1.00
231_K	235_E	2.428	1.00
64_A	98_A	2.427	1.00
60_L	72_L	2.412	1.00
286_T	289_E	2.410	1.00
228_A	233_E	2.284	1.00
205_R	209_A	2.280	1.00
200_L	204_R	2.235	1.00
136_E	183_L	2.234	1.00
177_A	202_E	2.168	1.00
30_Q	34_E	2.163	1.00
323_Q	327_D	2.148	1.00
202_E	206_A	2.131	1.00
197_E	201_K	2.093	1.00
207_F	217_A	2.084	1.00
26_V	30_Q	2.075	1.00
232_E	236_K	2.067	1.00
23_Q	99_P	2.065	1.00
35_C	326_S	2.048	1.00
29_A	63_L	2.022	1.00
200_L	219_F	2.017	1.00
229_H	328_A	2.010	1.00
95_S	100_G	1.947	1.00
41_W	73_A	1.937	1.00
91_F	102_I	1.935	1.00
27_K	30_Q	1.920	1.00
296_R	300_T	1.917	1.00
143_R	164_K	1.915	1.00
64_A	72_L	1.867	1.00
40_F	70_I	1.853	1.00
181_A	206_A	1.846	1.00
55_A	90_Q	1.835	1.00
239_V	243_S	1.834	1.00
283_I	290_V	1.815	1.00
178_I	209_A	1.770	1.00
26_V	66_S	1.752	1.00
197_E	300_T	1.729	1.00
139_T	164_K	1.717	1.00
114_Q	118_D	1.712	1.00
198_E	201_K	1.669	1.00
91_F	104_L	1.664	1.00
29_A	40_F	1.664	1.00
202_E	205_R	1.641	1.00
206_A	209_A	1.623	1.00
171_G	187_F	1.615	1.00
136_E	140_H	1.602	1.00
289_E	292_E	1.586	1.00
63_L	72_L	1.583	1.00
31_M	35_C	1.571	1.00
227_A	290_V	1.563	1.00
288_E	292_E	1.553	1.00
139_T	183_L	1.500	1.00
29_A	67_T	1.497	1.00
17_T	20_D	1.485	1.00
26_V	62_Y	1.468	1.00
221_L	303_I	1.458	1.00
291_A	295_T	1.455	1.00
233_E	237_H	1.455	1.00
295_T	298_S	1.441	1.00
33_E	67_T	1.429	1.00
207_F	212_P	1.429	1.00
178_I	182_K	1.409	1.00
34_E	68_R	1.400	1.00
324_L	328_A	1.392	1.00
42_V	60_L	1.388	1.00
147_P	150_H	1.377	1.00
140_H	144_D	1.375	1.00
139_T	167_I	1.362	1.00
140_H	145_D	1.361	1.00
23_Q	27_K	1.360	1.00
62_Y	97_L	1.346	1.00
218_E	304_N	1.323	1.00
62_Y	65_A	1.317	1.00
132_D	183_L	1.314	1.00
55_A	58_V	1.295	1.00
82_Y	90_Q	1.286	1.00
87_V	134_K	1.285	1.00
227_A	287_K	1.282	1.00
236_K	239_V	1.277	1.00
73_A	103_D	1.269	1.00
20_D	24_H	1.268	1.00
255_N	259_R	1.268	1.00
254_V	257_G	1.266	1.00
289_E	293_E	1.264	1.00
136_E	149_T	1.262	1.00
168_F	220_H	1.260	1.00
287_K	324_L	1.255	1.00
292_E	296_R	1.245	1.00
135_L	183_L	1.229	1.00
33_E	68_R	1.225	1.00
226_F	237_H	1.216	1.00
233_E	236_K	1.216	1.00
228_A	234_A	1.215	1.00
168_F	186_S	1.209	1.00
54_S	93_L	1.203	1.00
181_A	210_H	1.191	1.00
178_I	210_H	1.177	1.00
132_D	136_E	1.173	1.00
174_T	202_E	1.163	1.00
139_T	185_I	1.161	1.00
236_K	240_S	1.158	1.00
35_C	322_Y	1.157	1.00
27_K	31_M	1.142	1.00
285_G	290_V	1.142	1.00
94_L	102_I	1.141	1.00
60_L	74_S	1.138	1.00
207_F	214_G	1.136	1.00
175_E	178_I	1.136	1.00
238_I	242_E	1.132	1.00
29_A	70_I	1.130	1.00
106_V	135_L	1.126	1.00
104_L	138_L	1.126	1.00
182_K	210_H	1.122	1.00
138_L	142_V	1.119	1.00
256_V	259_R	1.102	1.00
126_K	129_R	1.095	1.00
42_V	63_L	1.094	1.00
227_A	324_L	1.092	1.00
260_E	263_E	1.085	1.00
86_K	90_Q	1.082	1.00
129_R	175_E	1.080	1.00
113_F	116_S	1.072	1.00
218_E	305_D	1.067	1.00
178_I	202_E	1.066	1.00
229_H	233_E	1.065	1.00
57_E	90_Q	1.063	1.00
99_P	160_Q	1.062	1.00
58_V	61_G	1.056	1.00
235_E	239_V	1.053	1.00
34_E	323_Q	1.048	1.00
62_Y	66_S	1.040	1.00
206_A	210_H	1.038	1.00
30_Q	68_R	1.034	1.00
152_Y	155_L	1.019	1.00
255_N	258_S	1.014	1.00
24_H	27_K	1.013	1.00
95_S	161_V	1.007	1.00
58_V	94_L	1.005	1.00
27_K	315_A	1.003	1.00
37_Y	326_S	1.002	1.00
232_E	235_E	1.000	1.00
198_E	202_E	0.997	1.00
76_G	170_L	0.995	1.00
283_I	293_E	0.991	1.00
177_A	206_A	0.986	1.00
308_I	325_L	0.982	1.00
32_A	322_Y	0.974	1.00
193_I	196_E	0.973	1.00
180_A	187_F	0.972	1.00
225_V	308_I	0.963	1.00
254_V	259_R	0.961	1.00
95_S	163_R	0.954	1.00
223_P	283_I	0.951	1.00
179_S	183_L	0.951	1.00
137_E	140_H	0.951	1.00
322_Y	326_S	0.949	1.00
111_G	116_S	0.948	1.00
132_D	179_S	0.948	1.00
139_T	143_R	0.948	1.00
39_R	73_A	0.947	1.00
130_Q	133_E	0.947	1.00
112_G	116_S	0.945	1.00
19_A	23_Q	0.943	1.00
57_E	77_V	0.939	1.00
188_V	220_H	0.934	1.00
321_S	324_L	0.930	1.00
228_A	237_H	0.928	1.00
24_H	315_A	0.923	1.00
126_K	130_Q	0.922	1.00
123_E	126_K	0.915	1.00
230_T	234_A	0.915	1.00
134_K	138_L	0.912	1.00
79_L	87_V	0.911	1.00
270_T	273_Y	0.906	1.00
133_E	137_E	0.906	1.00
249_K	253_K	0.904	1.00
204_R	208_D	0.902	1.00
84_S	137_E	0.901	1.00
238_I	284_A	0.894	1.00
200_L	203_A	0.881	1.00
197_E	301_Y	0.873	1.00
207_F	210_H	0.872	1.00
146_F	149_T	0.870	1.00
27_K	34_E	0.869	1.00
64_A	102_I	0.867	1.00
295_T	300_T	0.867	1.00
23_Q	26_V	0.864	1.00
158_R	161_V	0.859	1.00
177_A	181_A	0.858	1.00
130_Q	134_K	0.855	1.00
235_E	279_K	0.854	1.00
292_E	295_T	0.854	1.00
142_V	165_P	0.850	1.00
137_E	149_T	0.848	1.00
108_K	127_P	0.841	1.00
22_L	97_L	0.840	1.00
61_G	65_A	0.839	1.00
237_H	324_L	0.838	1.00
229_H	324_L	0.829	1.00
39_R	305_D	0.828	1.00
208_D	214_G	0.827	1.00
187_F	203_A	0.826	1.00
240_S	244_I	0.826	1.00
76_G	107_G	0.826	1.00
95_S	164_K	0.823	1.00
223_P	294_L	0.821	1.00
237_H	240_S	0.818	1.00
146_F	150_H	0.817	1.00
200_L	301_Y	0.817	1.00
148_D	152_Y	0.816	1.00
79_L	134_K	0.811	1.00
60_L	64_A	0.810	1.00
204_R	219_F	0.807	1.00
34_E	327_D	0.806	1.00
96_A	163_R	0.799	1.00
46_H	89_E	0.793	1.00
225_V	325_L	0.791	1.00
153_A	158_R	0.790	1.00
310_T	325_L	0.788	1.00
181_A	207_F	0.787	1.00
141_F	147_P	0.782	1.00
169_L	180_A	0.779	1.00
242_E	245_K	0.777	1.00
207_F	215_S	0.776	1.00
146_F	154_A	0.776	1.00
96_A	160_Q	0.775	1.00
132_D	175_E	0.773	1.00
240_S	243_S	0.770	1.00
258_S	261_Q	0.770	1.00
22_L	62_Y	0.770	1.00
274_D	278_Q	0.769	1.00
146_F	152_Y	0.767	1.00
21_T	24_H	0.763	1.00
60_L	102_I	0.763	1.00
239_V	242_E	0.757	1.00
250_D	253_K	0.756	1.00
177_A	187_F	0.755	1.00
26_V	63_L	0.754	1.00
136_E	182_K	0.751	1.00
114_Q	124_Y	0.749	1.00
257_G	260_E	0.747	1.00
60_L	94_L	0.747	1.00
64_A	94_L	0.745	1.00
65_A	98_A	0.744	1.00
41_W	75_G	0.744	1.00
219_F	303_I	0.744	1.00
263_E	270_T	0.742	1.00
140_H	147_P	0.741	1.00
253_K	257_G	0.740	1.00
189_F	199_V	0.735	1.00
152_Y	157_P	0.733	1.00
203_A	217_A	0.732	1.00
23_Q	68_R	0.729	1.00
128_V	175_E	0.728	1.00
95_S	162_D	0.727	1.00
78_M	111_G	0.727	1.00
204_R	207_F	0.725	1.00
310_T	322_Y	0.724	1.00
125_K	175_E	0.722	1.00
91_F	142_V	0.719	1.00
247_V	250_D	0.718	1.00
203_A	207_F	0.717	1.00
103_D	168_F	0.714	1.00
161_V	164_K	0.714	1.00
235_E	238_I	0.709	1.00
44_E	82_Y	0.708	1.00
115_L	118_D	0.708	1.00
169_L	176_S	0.708	1.00
274_D	277_V	0.707	1.00
169_L	184_G	0.701	1.00
87_V	138_L	0.695	1.00
171_G	176_S	0.690	1.00
61_G	94_L	0.689	1.00
201_K	302_K	0.687	1.00
76_G	87_V	0.687	1.00
169_L	179_S	0.686	1.00
38_H	69_K	0.684	1.00
23_Q	65_A	0.684	1.00
73_A	168_F	0.682	1.00
225_V	283_I	0.680	1.00
248_L	253_K	0.679	1.00
74_S	102_I	0.677	1.00
220_H	305_D	0.676	1.00
174_T	178_I	0.673	1.00
92_H	155_L	0.671	1.00
84_S	134_K	0.670	1.00
151_R	154_A	0.670	1.00
207_F	216_E	0.668	1.00
259_R	263_E	0.665	1.00
153_A	161_V	0.665	1.00
24_H	28_L	0.664	1.00
57_E	91_F	0.664	1.00
28_L	322_Y	0.663	1.00
40_F	63_L	0.659	1.00
178_I	205_R	0.658	1.00
71_R	166_G	0.656	1.00
298_S	303_I	0.655	1.00
140_H	143_R	0.655	1.00
39_R	307_V	0.655	1.00
140_H	149_T	0.655	1.00
212_P	215_S	0.651	1.00
254_V	258_S	0.650	1.00
157_P	161_V	0.649	1.00
153_A	156_R	0.649	1.00
235_E	284_A	0.648	1.00
31_M	326_S	0.648	1.00
153_A	157_P	0.647	1.00
106_V	138_L	0.647	1.00
246_V	250_D	0.645	1.00
133_E	136_E	0.644	1.00
72_L	98_A	0.642	1.00
83_S	86_K	0.637	1.00
95_S	98_A	0.636	1.00
157_P	160_Q	0.636	1.00
92_H	157_P	0.635	1.00
85_Y	141_F	0.635	1.00
67_T	101_R	0.632	1.00
26_V	29_A	0.632	1.00
82_Y	86_K	0.629	1.00
288_E	291_A	0.626	1.00
175_E	179_S	0.624	1.00
228_A	231_K	0.624	1.00
26_V	65_A	0.623	1.00
205_R	208_D	0.623	1.00
229_H	287_K	0.623	1.00
32_A	70_I	0.622	1.00
182_K	209_A	0.622	1.00
231_K	234_A	0.622	1.00
273_Y	276_I	0.622	1.00
204_R	214_G	0.617	1.00
201_K	204_R	0.617	1.00
148_D	151_R	0.617	1.00
152_Y	161_V	0.616	1.00
18_A	21_T	0.614	1.00
108_K	131_F	0.614	1.00
244_I	247_V	0.613	1.00
174_T	206_A	0.613	1.00
38_H	71_R	0.613	1.00
92_H	142_V	0.610	1.00
42_V	59_L	0.610	1.00
276_I	280_T	0.608	1.00
182_K	206_A	0.607	1.00
59_L	93_L	0.603	1.00
136_E	139_T	0.602	1.00
61_G	98_A	0.601	1.00
257_G	261_Q	0.600	1.00
135_L	169_L	0.600	1.00
105_G	170_L	0.599	1.00
222_A	307_V	0.599	1.00
155_L	158_R	0.597	1.00
22_L	26_V	0.592	1.00
204_R	304_N	0.592	1.00
192_F	196_E	0.590	1.00
67_T	70_I	0.590	1.00
168_F	218_E	0.586	1.00
287_K	328_A	0.585	1.00
114_Q	117_T	0.585	1.00
294_L	306_F	0.585	1.00
166_G	218_E	0.584	1.00
294_L	308_I	0.583	1.00
95_S	165_P	0.581	1.00
287_K	291_A	0.581	1.00
210_H	214_G	0.576	1.00
227_A	325_L	0.573	1.00
33_E	70_I	0.569	1.00
20_D	23_Q	0.567	1.00
117_T	124_Y	0.565	1.00
216_E	304_N	0.565	1.00
246_V	249_K	0.564	1.00
82_Y	87_V	0.562	1.00
92_H	160_Q	0.561	1.00
106_V	167_I	0.561	1.00
221_L	297_L	0.557	1.00
128_V	179_S	0.555	1.00
152_Y	156_R	0.554	1.00
95_S	159_P	0.552	1.00
203_A	219_F	0.552	1.00
61_G	64_A	0.551	1.00
198_E	205_R	0.550	1.00
84_S	138_L	0.548	0.99
172_G	191_Y	0.543	0.99
288_E	328_A	0.542	0.99
177_A	203_A	0.542	0.99
172_G	199_V	0.541	0.99
88_A	142_V	0.540	0.99
83_S	122_A	0.540	0.99
214_G	217_A	0.538	0.99
194_N	296_R	0.538	0.99
219_F	304_N	0.537	0.99
71_R	161_V	0.533	0.99
56_P	74_S	0.531	0.99
154_A	157_P	0.531	0.99
310_T	321_S	0.528	0.99
98_A	102_I	0.528	0.99
243_S	247_V	0.527	0.99
191_Y	194_N	0.526	0.99
227_A	286_T	0.525	0.99
25_T	28_L	0.523	0.99
223_P	306_F	0.522	0.99
58_V	93_L	0.522	0.99
199_V	202_E	0.520	0.99
250_D	271_E	0.519	0.99
249_K	252_R	0.519	0.99
228_A	324_L	0.519	0.99
275_I	278_Q	0.519	0.99
293_E	297_L	0.517	0.99
137_E	147_P	0.517	0.99
45_H	116_S	0.516	0.99
92_H	96_A	0.516	0.99
122_A	130_Q	0.516	0.99
79_L	106_V	0.515	0.99
113_F	117_T	0.515	0.99
277_V	280_T	0.515	0.99
297_L	301_Y	0.514	0.99
62_Y	98_A	0.512	0.99
230_T	236_K	0.511	0.99
39_R	71_R	0.511	0.99
156_R	161_V	0.510	0.99
106_V	169_L	0.510	0.99
152_Y	158_R	0.508	0.99
176_S	179_S	0.508	0.99
204_R	215_S	0.506	0.99
225_V	290_V	0.505	0.99
118_D	151_R	0.504	0.99
168_F	305_D	0.504	0.99
253_K	259_R	0.503	0.99
34_E	69_K	0.503	0.99
135_L	179_S	0.502	0.99
131_F	169_L	0.501	0.99
135_L	139_T	0.501	0.99
247_V	252_R	0.501	0.99
224_A	309_F	0.500	0.99
75_G	188_V	0.500	0.99

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
1lucA	1	0.9401	100	0.173	Contact Map
2wgkA	2	0.979	100	0.184	Contact Map
1lucB	1	0.9311	100	0.197	Contact Map
2i7gA	2	0.9611	100	0.205	Contact Map
4us5A	3	0.9611	100	0.225	Contact Map
3raoA	2	0.9611	100	0.237	Contact Map
1ezwA	3	0.9431	100	0.238	Contact Map
3c8nA	2	0.9401	100	0.238	Contact Map
1rhcA	2	0.9341	100	0.24	Contact Map
1z69A	4	0.9311	100	0.246	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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