YBDK - BACSU - GREMLIN Contacts

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YBDK - Sensor histidine kinase YbdK

UniProt:	O31433	Sequences: MLLFTAVISVPMLLLAVSVLMSVIYDSMFKPMNHGMPFHRSFAYPAMIVVFLISLLLLAFLFSKSIHSLLHKINLLNQTIRHLASDQRVPDKIEVKRADEIGELIKSVNLLIERTTYRELELRQQEEIKKELLQKLRHDINTPLTALRLQLFYLEDQCHGQAVFESLYQQIEYISELTNEFNLYSAETLESSYIVNEEVRLNELLETAVKKWDYLYSMSGIELHYKPADQDVIWMSNTLWMERLFDNIFQNTLRHSKAKKMEVTIEHGDVFIRDDGIGFDRNESSEGLGLKIIEDTCRLLAITYELHTNDNGTGFLFSKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	320 (274)
Sequences:	65573 (52369)
Seq/√Len:	3163.8

ECOLI - TORS BARA RCSD GLRK QSEC YEDV CUSS BAES CPXA RCSC PHOQ BASS CREC ARCB RSTB ENVZ NARQ NARX EVGS ATOS ZRAS PHOR UHPB KDPD DCUS YPDA DPIB NTRB
BACSU - YBDK YCLK YVRG YVCQ CSSS YRKQ KINB YCBM YKOH RESE YYCG YXDK BCES PHOR KINE LIAS GLNK YESM KINA KIND KINC YFIJ LYTS YXJM DEGS YWPD COMP DCTS CITS MALK YDFH YHCY DESK YVFT NATK
HALSA - Q9HQ15 Q9HQE9 Q9HQG5 Q9HQ16 O51970 Q9HRE4 BAT Q9HR10 Q9HRG1 Q9HNM2 Q9HNA6 Q9HQB9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
199_V	236_S	3.685	1.00
273_R	314_G	3.592	1.00
274_D	278_G	3.522	1.00
305_E	316_L	3.362	1.00
294_E	298_R	3.205	1.00
151_L	167_L	3.115	1.00
271_F	314_G	2.939	1.00
236_S	300_L	2.894	1.00
256_S	275_D	2.840	1.00
155_E	168_Y	2.693	1.00
264_T	271_F	2.691	1.00
198_E	235_M	2.663	1.00
148_R	172_E	2.594	1.00
271_F	316_L	2.571	1.00
224_H	262_E	2.523	1.00
306_L	315_F	2.476	1.00
226_K	264_T	2.468	1.00
198_E	233_I	2.437	1.00
148_R	171_I	2.315	1.00
244_L	297_C	2.306	1.00
155_E	165_E	2.292	1.00
293_I	304_Y	2.258	1.00
262_E	273_R	2.228	1.00
307_H	316_L	2.161	1.00
297_C	302_I	2.136	1.00
200_R	203_E	2.109	1.00
207_T	242_E	2.078	1.00
264_T	273_R	2.062	1.00
197_E	238_T	2.053	1.00
307_H	314_G	2.051	1.00
148_R	175_S	2.031	1.00
266_E	271_F	2.017	1.00
250_Q	254_R	2.009	1.00
212_W	246_D	1.979	1.00
175_S	179_N	1.955	1.00
308_T	313_T	1.936	1.00
226_K	262_E	1.931	1.00
196_N	235_M	1.896	1.00
147_L	171_I	1.892	1.00
297_C	317_F	1.836	1.00
303_T	318_S	1.814	1.00
236_S	241_M	1.798	1.00
244_L	296_T	1.745	1.00
244_L	293_I	1.736	1.00
216_Y	253_L	1.709	1.00
152_F	168_Y	1.703	1.00
139_D	243_R	1.646	1.00
298_R	303_T	1.601	1.00
279_F	313_T	1.595	1.00
119_E	123_R	1.581	1.00
296_T	300_L	1.570	1.00
305_E	318_S	1.544	1.00
168_Y	172_E	1.524	1.00
155_E	161_Q	1.518	1.00
126_E	129_K	1.516	1.00
157_Q	160_G	1.511	1.00
150_Q	163_V	1.500	1.00
151_L	168_Y	1.489	1.00
237_N	240_W	1.487	1.00
256_S	260_K	1.482	1.00
202_N	206_E	1.466	1.00
211_K	242_E	1.449	1.00
247_N	293_I	1.448	1.00
245_F	270_V	1.439	1.00
147_L	167_L	1.407	1.00
99_D	102_G	1.404	1.00
260_K	275_D	1.403	1.00
240_W	243_R	1.386	1.00
98_A	102_G	1.386	1.00
154_L	164_F	1.379	1.00
256_S	261_M	1.375	1.00
148_R	168_Y	1.354	1.00
200_R	233_I	1.353	1.00
194_I	237_N	1.345	1.00
207_T	238_T	1.327	1.00
262_E	275_D	1.316	1.00
270_V	317_F	1.307	1.00
213_D	217_S	1.287	1.00
200_R	231_D	1.285	1.00
119_E	122_L	1.277	1.00
150_Q	166_S	1.260	1.00
241_M	300_L	1.257	1.00
238_T	242_E	1.254	1.00
131_E	135_K	1.251	1.00
308_T	311_N	1.249	1.00
146_A	170_Q	1.237	1.00
127_E	131_E	1.231	1.00
62_F	66_I	1.227	1.00
297_C	304_Y	1.223	1.00
176_E	239_L	1.220	1.00
151_L	171_I	1.217	1.00
196_N	300_L	1.212	1.00
240_W	296_T	1.211	1.00
206_E	225_Y	1.200	1.00
105_I	109_N	1.200	1.00
202_N	231_D	1.199	1.00
274_D	312_G	1.195	1.00
82_H	88_R	1.167	1.00
154_L	160_G	1.159	1.00
227_P	265_I	1.156	1.00
69_L	72_K	1.147	1.00
209_V	225_Y	1.142	1.00
129_K	133_L	1.138	1.00
240_W	299_L	1.137	1.00
109_N	112_I	1.130	1.00
165_E	169_Q	1.124	1.00
257_K	260_K	1.124	1.00
295_D	298_R	1.118	1.00
208_A	246_D	1.117	1.00
208_A	242_E	1.107	1.00
97_R	102_G	1.101	1.00
302_I	317_F	1.096	1.00
215_L	218_M	1.092	1.00
104_L	108_V	1.088	1.00
202_N	265_I	1.087	1.00
60_F	64_K	1.087	1.00
244_L	317_F	1.085	1.00
170_Q	173_Y	1.084	1.00
116_T	120_L	1.084	1.00
302_I	319_K	1.083	1.00
149_L	153_Y	1.082	1.00
204_L	236_S	1.076	1.00
59_A	63_S	1.072	1.00
118_R	121_E	1.062	1.00
141_N	179_N	1.057	1.00
77_N	81_R	1.051	1.00
211_K	246_D	1.048	1.00
194_I	240_W	1.048	1.00
146_A	150_Q	1.040	1.00
199_V	204_L	1.036	1.00
151_L	155_E	1.022	1.00
212_W	249_F	1.010	1.00
132_L	136_L	1.006	1.00
101_I	105_I	1.003	1.00
151_L	164_F	1.001	1.00
204_L	208_A	0.999	1.00
205_L	265_I	0.998	1.00
273_R	309_N	0.995	1.00
306_L	313_T	0.994	1.00
124_Q	128_I	0.981	1.00
179_N	183_L	0.981	1.00
121_E	124_Q	0.977	1.00
108_V	111_L	0.977	1.00
215_L	250_Q	0.961	1.00
115_T	119_E	0.959	1.00
101_I	104_L	0.957	1.00
80_I	83_L	0.956	1.00
118_R	122_L	0.955	1.00
166_S	170_Q	0.955	1.00
295_D	299_L	0.954	1.00
278_G	313_T	0.948	1.00
111_L	115_T	0.946	1.00
123_R	127_E	0.943	1.00
160_G	163_V	0.941	1.00
180_E	240_W	0.940	1.00
114_R	117_Y	0.936	1.00
208_A	212_W	0.934	1.00
162_A	166_S	0.932	1.00
74_N	77_N	0.930	1.00
195_V	237_N	0.925	1.00
126_E	130_K	0.925	1.00
202_N	227_P	0.924	1.00
274_D	313_T	0.921	1.00
255_H	277_I	0.919	1.00
184_Y	291_K	0.916	1.00
127_E	130_K	0.914	1.00
221_I	256_S	0.911	1.00
113_E	117_Y	0.909	1.00
161_Q	165_E	0.908	1.00
209_V	213_D	0.907	1.00
172_E	175_S	0.903	1.00
228_A	266_E	0.901	1.00
169_Q	207_T	0.896	1.00
148_R	152_F	0.896	1.00
120_L	124_Q	0.892	1.00
80_I	84_A	0.888	1.00
105_I	108_V	0.887	1.00
171_I	175_S	0.884	1.00
196_N	301_A	0.884	1.00
173_Y	242_E	0.876	1.00
183_L	243_R	0.873	1.00
146_A	149_L	0.871	1.00
117_Y	121_E	0.869	1.00
242_E	246_D	0.867	1.00
45_P	49_V	0.867	1.00
120_L	123_R	0.864	1.00
245_F	249_F	0.857	1.00
180_E	243_R	0.854	1.00
200_R	232_V	0.848	1.00
252_T	261_M	0.847	1.00
247_N	250_Q	0.844	1.00
196_N	236_S	0.844	1.00
140_I	174_I	0.842	1.00
239_L	242_E	0.837	1.00
108_V	112_I	0.835	1.00
83_L	112_I	0.834	1.00
115_T	118_R	0.828	1.00
201_L	270_V	0.825	1.00
209_V	223_L	0.824	1.00
130_K	188_T	0.822	1.00
102_G	106_K	0.821	1.00
203_E	207_T	0.819	1.00
165_E	168_Y	0.816	1.00
166_S	169_Q	0.815	1.00
88_R	91_D	0.806	1.00
66_I	70_L	0.805	1.00
82_H	91_D	0.802	1.00
294_E	303_T	0.801	1.00
246_D	250_Q	0.799	1.00
66_I	69_L	0.799	1.00
248_I	315_F	0.796	1.00
248_I	293_I	0.787	1.00
121_E	125_Q	0.787	1.00
167_L	171_I	0.783	1.00
279_F	308_T	0.781	1.00
142_T	146_A	0.780	1.00
281_R	308_T	0.780	1.00
245_F	272_I	0.778	1.00
254_R	285_S	0.778	1.00
271_F	307_H	0.775	1.00
104_L	107_S	0.766	1.00
199_V	238_T	0.764	1.00
220_G	259_K	0.764	1.00
293_I	297_C	0.762	1.00
114_R	118_R	0.759	1.00
288_L	292_I	0.757	1.00
153_Y	157_Q	0.756	1.00
141_N	175_S	0.754	1.00
212_W	250_Q	0.753	1.00
77_N	103_E	0.750	1.00
162_A	165_E	0.749	1.00
102_G	105_I	0.742	1.00
176_E	180_E	0.735	1.00
194_I	299_L	0.729	1.00
122_L	125_Q	0.727	1.00
64_K	68_S	0.727	1.00
92_K	112_I	0.724	1.00
77_N	107_S	0.724	1.00
274_D	277_I	0.722	1.00
216_Y	223_L	0.722	1.00
155_E	164_F	0.722	1.00
279_F	315_F	0.721	1.00
214_Y	217_S	0.721	1.00
216_Y	220_G	0.719	1.00
125_Q	129_K	0.718	1.00
72_K	76_L	0.715	1.00
163_V	166_S	0.715	1.00
248_I	317_F	0.713	1.00
243_R	296_T	0.712	1.00
210_K	213_D	0.711	1.00
183_L	240_W	0.710	1.00
206_E	210_K	0.710	1.00
67_H	71_H	0.708	1.00
221_I	253_L	0.708	1.00
208_A	249_F	0.704	1.00
144_L	178_T	0.703	1.00
92_K	113_E	0.702	1.00
123_R	126_E	0.700	1.00
202_N	230_Q	0.698	1.00
205_L	245_F	0.698	1.00
150_Q	170_Q	0.698	1.00
73_I	76_L	0.697	1.00
279_F	306_L	0.697	1.00
138_H	247_N	0.694	1.00
136_L	181_F	0.688	1.00
182_N	186_A	0.688	1.00
248_I	304_Y	0.687	1.00
116_T	119_E	0.681	1.00
221_I	261_M	0.677	1.00
107_S	110_L	0.676	1.00
220_G	258_A	0.676	1.00
81_R	107_S	0.675	1.00
199_V	235_M	0.673	1.00
79_T	82_H	0.671	1.00
139_D	247_N	0.670	1.00
244_L	300_L	0.667	1.00
94_E	109_N	0.666	1.00
222_E	225_Y	0.658	1.00
257_K	277_I	0.654	1.00
80_I	107_S	0.650	1.00
312_G	315_F	0.648	1.00
97_R	105_I	0.647	1.00
170_Q	211_K	0.637	1.00
297_C	319_K	0.634	1.00
305_E	317_F	0.633	1.00
63_S	67_H	0.633	1.00
75_L	79_T	0.631	1.00
44_Y	48_I	0.628	1.00
192_S	240_W	0.628	1.00
248_I	297_C	0.625	1.00
240_W	300_L	0.622	1.00
249_F	263_V	0.619	1.00
145_T	149_L	0.618	1.00
133_L	137_R	0.617	1.00
277_I	283_E	0.616	1.00
252_T	272_I	0.616	1.00
139_D	143_P	0.613	1.00
73_I	77_N	0.612	1.00
152_F	156_D	0.611	1.00
256_S	259_K	0.611	1.00
84_A	87_Q	0.608	1.00
212_W	253_L	0.607	1.00
201_L	234_W	0.607	1.00
203_E	238_T	0.607	1.00
216_Y	221_I	0.606	1.00
217_S	220_G	0.605	1.00
159_H	163_V	0.605	1.00
204_L	241_M	0.604	1.00
104_L	111_L	0.603	1.00
78_Q	82_H	0.600	1.00
150_Q	167_L	0.598	1.00
90_P	94_E	0.597	1.00
124_Q	127_E	0.596	1.00
74_N	78_Q	0.596	1.00
91_D	94_E	0.595	1.00
103_E	106_K	0.595	1.00
228_A	232_V	0.594	1.00
107_S	111_L	0.594	1.00
76_L	80_I	0.594	1.00
154_L	163_V	0.592	1.00
105_I	112_I	0.591	1.00
153_Y	158_C	0.590	1.00
206_E	227_P	0.590	1.00
100_E	104_L	0.588	1.00
122_L	126_E	0.586	1.00
216_Y	261_M	0.585	1.00
138_H	142_T	0.583	1.00
205_L	263_V	0.581	1.00
99_D	103_E	0.581	1.00
273_R	310_D	0.580	1.00
164_F	168_Y	0.579	1.00
95_V	106_K	0.577	1.00
79_T	93_I	0.576	1.00
45_P	48_I	0.574	1.00
202_N	232_V	0.574	1.00
146_A	166_S	0.572	1.00
226_K	266_E	0.572	1.00
68_S	71_H	0.572	1.00
281_R	309_N	0.570	1.00
110_L	114_R	0.569	1.00
228_A	265_I	0.569	1.00
254_R	283_E	0.567	1.00
112_I	116_T	0.567	1.00
204_L	242_E	0.566	1.00
90_P	116_T	0.566	1.00
172_E	176_E	0.565	1.00
81_R	84_A	0.564	1.00
188_T	295_D	0.564	1.00
97_R	100_E	0.564	1.00
135_K	139_D	0.563	1.00
210_K	214_Y	0.562	1.00
160_G	164_F	0.561	1.00
98_A	101_I	0.560	1.00
205_L	208_A	0.560	1.00
158_C	161_Q	0.559	1.00
89_V	93_I	0.558	1.00
153_Y	163_V	0.557	1.00
291_K	295_D	0.555	1.00
81_R	103_E	0.553	1.00
60_F	63_S	0.552	1.00
206_E	209_V	0.551	1.00
168_Y	171_I	0.551	1.00
208_A	211_K	0.550	1.00
91_D	95_V	0.549	1.00
304_Y	315_F	0.548	1.00
243_R	246_D	0.547	1.00
69_L	73_I	0.547	1.00
216_Y	219_S	0.544	1.00
84_A	110_L	0.543	1.00
98_A	104_L	0.543	1.00
184_Y	188_T	0.542	1.00
219_S	253_L	0.541	1.00
207_T	211_K	0.540	1.00
82_H	86_D	0.540	1.00
103_E	107_S	0.540	1.00
83_L	87_Q	0.539	1.00
139_D	177_L	0.538	1.00
49_V	53_I	0.538	1.00
221_I	260_K	0.536	1.00
275_D	311_N	0.533	1.00
131_E	295_D	0.532	1.00
251_N	289_G	0.531	1.00
132_L	139_D	0.529	1.00
214_Y	218_M	0.525	1.00
79_T	91_D	0.523	1.00
232_V	265_I	0.523	1.00
221_I	275_D	0.521	1.00
72_K	75_L	0.519	1.00
221_I	225_Y	0.518	1.00
80_I	108_V	0.516	1.00
263_V	272_I	0.515	1.00
113_E	116_T	0.515	1.00
52_L	56_L	0.514	1.00
104_L	109_N	0.514	1.00
95_V	98_A	0.513	1.00
44_Y	47_M	0.512	1.00
70_L	74_N	0.512	1.00
112_I	115_T	0.510	1.00
155_E	158_C	0.510	1.00
68_S	72_K	0.508	1.00
106_K	110_L	0.507	1.00
215_L	219_S	0.507	1.00
105_I	111_L	0.505	1.00
87_Q	91_D	0.505	1.00
139_D	292_I	0.504	1.00
97_R	104_L	0.504	1.00
142_T	149_L	0.504	1.00
174_I	178_T	0.504	1.00
278_G	312_G	0.504	1.00
197_E	239_L	0.501	1.00
203_E	206_E	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
4i5sA	2	0.7906	100	0.338	Contact Map
4bixA	2	0.6469	100	0.387	Contact Map
4ctiA	2	0.6937	100	0.424	Contact Map
4q20A	2	0.6469	100	0.457	Contact Map
3jz3A	2	0.4813	100	0.458	Contact Map
4mpcA	2	0.8469	100	0.462	Contact Map
2q8gA	2	0.8625	100	0.474	Contact Map
2c2aA	2	0.6531	100	0.474	Contact Map
4r39A	1	0.5938	100	0.476	Contact Map
4e01A	3	0.8156	100	0.482	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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