YKVP - BACSU - GREMLIN Contacts

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YKVP - Spore protein YkvP

UniProt:	O31681	Sequences: MKILFLESHPMWLYGLPNGFREAGHTVMISGPVSRENITEMIDEFKPDLIVSMGWTPEHSREKQAWIRNATKKVNIPLVYWATEDPLHTQNFTIPLIKKMKPDFVFTVTPSLCKTYESMGIKAAHLDFAFHESIHHQIKPLAKYSCDIAVVANAYPNFLEEHPEVFRSSSLKTLIRPLIRKGIRIDFWGRNWEKMSKYIGREIPRNWIHGYLDYTEAYKVYSSAKIIIGLQNCESQLTQRTYEILGSGGFLLTSDTPAVRGKFKPGRDLIVSSSPKETLEKVKYYLNHDSERKKIQINGKKAVKNDSYRHRAERMLEVLKSRGIIRNLGETIHYVDVLKEKYVIHHVTPGETLSIIASKYNVSLQQLMELNHFKSDQIYAGQIIKIREKLFRNINNKLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	399 (309)
Sequences:	25949 (21422)
Seq/√Len:	1218.7

ECOLI - RFAB WCAL RFAG GLGA WCAI WCAC WBBK
BACSU - YKVP YPJH YQGM YTCC EPSD COTSA EPSF TUAC GLGA CGEB
HALSA - Q9HRP8 Q9HQQ0 Q9HS45 Q9HSW1 Q9HSV4 Q9HSV2 Q9HRP9
SULSO - Q97V61 Q97UM0 Q97VL4 Q97XT7 Q980C8 Q97XT8 Q7LXI2 Q97V80 Q97ZD3 Q97XT1 Q97UU3 Q7LXM9 Q97XU2 Q97XT6 Q97XT9 Q97XF6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
149_A	224_A	4.701	1.00
184_R	207_W	3.512	1.00
104_F	124_A	3.314	1.00
51_V	319_L	3.197	1.00
227_I	244_I	2.954	1.00
147_D	186_D	2.757	1.00
145_S	184_R	2.726	1.00
181_K	283_K	2.614	1.00
2_K	26_T	2.605	1.00
177_P	279_L	2.524	1.00
194_K	198_Y	2.487	1.00
25_H	316_L	2.464	1.00
302_A	305_N	2.462	1.00
173_T	200_G	2.343	1.00
146_C	286_L	2.337	1.00
150_V	168_S	2.285	1.00
186_D	209_H	2.274	1.00
28_M	47_P	2.262	1.00
179_I	205_R	2.242	1.00
113_C	117_E	2.212	1.00
175_I	185_I	2.152	1.00
28_M	45_F	2.116	1.00
177_P	276_K	2.099	1.00
263_F	269_L	2.080	1.00
288_H	291_E	2.071	1.00
167_R	170_S	2.057	1.00
173_T	275_P	2.045	1.00
23_A	313_E	2.020	1.00
248_G	300_K	1.962	1.00
255_D	260_R	1.945	1.00
4_L	47_P	1.933	1.00
104_F	318_V	1.917	1.00
281_K	284_Y	1.888	1.00
292_R	296_Q	1.878	1.00
284_Y	291_E	1.869	1.00
264_K	267_R	1.833	1.00
255_D	273_S	1.828	1.00
147_D	184_R	1.827	1.00
188_W	220_V	1.803	1.00
124_A	321_S	1.800	1.00
270_I	281_K	1.795	1.00
148_I	226_I	1.779	1.00
273_S	277_E	1.774	1.00
23_A	316_L	1.773	1.00
200_G	204_P	1.766	1.00
4_L	30_S	1.743	1.00
268_D	302_A	1.742	1.00
200_G	203_I	1.686	1.00
316_L	320_K	1.675	1.00
176_R	204_P	1.672	1.00
284_Y	288_H	1.669	1.00
110_P	113_C	1.661	1.00
147_D	223_S	1.639	1.00
171_L	228_I	1.637	1.00
227_I	249_G	1.617	1.00
186_D	207_W	1.612	1.00
51_V	81_W	1.611	1.00
190_R	194_K	1.607	1.00
310_H	314_R	1.590	1.00
146_C	225_K	1.588	1.00
283_K	287_N	1.583	1.00
129_A	308_Y	1.569	1.00
80_Y	102_P	1.559	1.00
171_L	185_I	1.540	1.00
113_C	125_H	1.538	1.00
291_E	294_K	1.529	1.00
264_K	302_A	1.521	1.00
151_V	217_A	1.520	1.00
212_L	216_E	1.520	1.00
274_S	277_E	1.518	1.00
19_G	312_A	1.516	1.00
19_G	22_E	1.514	1.00
175_I	183_I	1.502	1.00
301_K	304_K	1.496	1.00
267_R	298_N	1.495	1.00
113_C	123_A	1.480	1.00
19_G	309_R	1.469	1.00
5_F	53_M	1.468	1.00
148_I	282_V	1.455	1.00
5_F	20_F	1.451	1.00
106_F	318_V	1.447	1.00
216_E	219_K	1.433	1.00
294_K	298_N	1.428	1.00
110_P	261_G	1.427	1.00
277_E	281_K	1.422	1.00
212_L	220_V	1.410	1.00
178_L	283_K	1.405	1.00
272_S	281_K	1.404	1.00
106_F	315_M	1.399	1.00
107_T	123_A	1.391	1.00
270_I	284_Y	1.373	1.00
14_Y	18_N	1.344	1.00
52_S	78_L	1.341	1.00
154_A	187_F	1.340	1.00
142_A	145_S	1.332	1.00
213_D	216_E	1.332	1.00
275_P	279_L	1.302	1.00
104_F	321_S	1.292	1.00
193_E	196_S	1.279	1.00
21_R	24_G	1.274	1.00
314_R	317_E	1.271	1.00
195_M	198_Y	1.259	1.00
201_R	204_P	1.254	1.00
253_T	259_V	1.249	1.00
148_I	228_I	1.245	1.00
264_K	268_D	1.243	1.00
188_W	209_H	1.242	1.00
298_N	301_K	1.224	1.00
5_F	17_P	1.221	1.00
170_S	275_P	1.211	1.00
110_P	125_H	1.190	1.00
201_R	208_I	1.179	1.00
147_D	225_K	1.172	1.00
241_T	259_V	1.164	1.00
277_E	280_E	1.160	1.00
110_P	114_K	1.153	1.00
293_K	297_I	1.152	1.00
285_Y	295_I	1.151	1.00
253_T	271_V	1.148	1.00
198_Y	203_I	1.145	1.00
224_A	249_G	1.143	1.00
186_D	220_V	1.143	1.00
177_P	275_P	1.138	1.00
296_Q	299_G	1.138	1.00
199_I	203_I	1.133	1.00
149_A	188_W	1.131	1.00
198_Y	201_R	1.120	1.00
289_D	292_R	1.118	1.00
167_R	232_N	1.108	1.00
237_L	242_Y	1.106	1.00
188_W	212_L	1.105	1.00
135_H	247_S	1.099	1.00
291_E	295_I	1.087	1.00
146_C	226_I	1.085	1.00
150_V	171_L	1.085	1.00
310_H	313_E	1.083	1.00
3_I	25_H	1.083	1.00
265_P	281_K	1.070	1.00
157_N	234_E	1.062	1.00
114_K	117_E	1.058	1.00
248_G	297_I	1.057	1.00
270_I	295_I	1.054	1.00
198_Y	202_E	1.053	1.00
174_L	278_T	1.049	1.00
311_R	314_R	1.044	1.00
134_I	218_Y	1.039	1.00
186_D	224_A	1.038	1.00
168_S	187_F	1.038	1.00
217_A	221_Y	1.034	1.00
12_W	239_Q	1.032	1.00
249_G	296_Q	1.031	1.00
176_R	180_R	1.027	1.00
231_Q	235_S	1.027	1.00
146_C	182_G	1.026	1.00
17_P	21_R	1.024	1.00
53_M	83_T	1.022	1.00
2_K	28_M	1.017	1.00
108_V	236_Q	1.016	1.00
169_S	200_G	1.014	1.00
124_A	318_V	1.012	1.00
209_H	212_L	1.011	1.00
307_S	310_H	1.005	1.00
214_Y	217_A	1.000	1.00
254_S	272_S	1.000	1.00
108_V	128_F	0.995	1.00
253_T	263_F	0.995	1.00
114_K	118_S	0.992	1.00
145_S	182_G	0.991	1.00
270_I	285_Y	0.985	1.00
238_T	259_V	0.982	1.00
229_G	241_T	0.981	1.00
132_E	307_S	0.981	1.00
107_T	113_C	0.980	1.00
229_G	240_R	0.974	1.00
19_G	23_A	0.970	1.00
149_A	220_V	0.965	1.00
177_P	181_K	0.964	1.00
169_S	173_T	0.960	1.00
222_S	247_S	0.957	1.00
230_L	278_T	0.953	1.00
83_T	239_Q	0.953	1.00
41_M	45_F	0.952	1.00
135_H	218_Y	0.951	1.00
190_R	211_Y	0.950	1.00
79_V	322_R	0.949	1.00
308_Y	311_R	0.947	1.00
146_C	183_I	0.946	1.00
245_L	299_G	0.944	1.00
17_P	29_I	0.941	1.00
12_W	83_T	0.934	1.00
52_S	80_Y	0.930	1.00
177_P	180_R	0.929	1.00
221_Y	247_S	0.929	1.00
296_Q	300_K	0.926	1.00
176_R	179_I	0.922	1.00
186_D	223_S	0.919	1.00
115_T	118_S	0.919	1.00
170_S	254_S	0.913	1.00
297_I	301_K	0.910	1.00
178_L	183_I	0.909	1.00
235_S	238_T	0.908	1.00
258_A	261_G	0.901	1.00
218_Y	247_S	0.900	1.00
36_E	40_E	0.894	1.00
218_Y	222_S	0.891	1.00
293_K	296_Q	0.889	1.00
147_D	224_A	0.886	1.00
195_M	199_I	0.880	1.00
126_L	318_V	0.874	1.00
102_P	105_V	0.872	1.00
155_Y	192_W	0.871	1.00
244_I	249_G	0.869	1.00
153_N	157_N	0.869	1.00
226_I	285_Y	0.866	1.00
78_L	102_P	0.861	1.00
151_V	221_Y	0.861	1.00
280_E	284_Y	0.857	1.00
289_D	293_K	0.857	1.00
276_K	280_E	0.854	1.00
245_L	251_L	0.852	1.00
295_I	298_N	0.850	1.00
279_L	283_K	0.838	1.00
39_T	73_K	0.835	1.00
270_I	291_E	0.834	1.00
227_I	240_R	0.832	1.00
183_I	286_L	0.831	1.00
313_E	316_L	0.830	1.00
13_L	53_M	0.829	1.00
313_E	317_E	0.828	1.00
174_L	279_L	0.827	1.00
107_T	116_Y	0.827	1.00
191_N	194_K	0.825	1.00
106_F	126_L	0.823	1.00
128_F	239_Q	0.821	1.00
5_F	27_V	0.817	1.00
7_E	13_L	0.816	1.00
131_H	135_H	0.813	1.00
79_V	106_F	0.813	1.00
49_L	319_L	0.807	1.00
148_I	175_I	0.806	1.00
11_M	15_G	0.802	1.00
124_A	314_R	0.800	1.00
170_S	173_T	0.798	1.00
131_H	134_I	0.797	1.00
209_H	220_V	0.796	1.00
16_L	315_M	0.793	1.00
311_R	315_M	0.790	1.00
178_L	282_V	0.789	1.00
12_W	128_F	0.789	1.00
15_G	308_Y	0.786	1.00
108_V	112_L	0.770	1.00
127_D	261_G	0.770	1.00
151_V	188_W	0.770	1.00
146_C	289_D	0.767	1.00
226_I	282_V	0.765	1.00
175_I	205_R	0.764	1.00
250_F	296_Q	0.763	1.00
15_G	18_N	0.752	1.00
196_S	200_G	0.751	1.00
71_T	78_L	0.750	1.00
126_L	315_M	0.748	1.00
173_T	176_R	0.747	1.00
129_A	311_R	0.745	1.00
268_D	299_G	0.745	1.00
21_R	27_V	0.744	1.00
229_G	259_V	0.743	1.00
39_T	43_D	0.739	1.00
228_I	282_V	0.738	1.00
149_A	221_Y	0.737	1.00
150_V	187_F	0.735	1.00
172_K	201_R	0.732	1.00
295_I	299_G	0.732	1.00
79_V	319_L	0.729	1.00
42_I	47_P	0.727	1.00
104_F	322_R	0.727	1.00
196_S	199_I	0.722	1.00
66_W	69_N	0.722	1.00
257_P	260_R	0.721	1.00
107_T	112_L	0.720	1.00
201_R	206_N	0.714	1.00
2_K	47_P	0.711	1.00
5_F	319_L	0.710	1.00
181_K	287_N	0.709	1.00
238_T	241_T	0.703	1.00
250_F	285_Y	0.698	1.00
317_E	320_K	0.697	1.00
138_I	222_S	0.696	1.00
150_V	227_I	0.695	1.00
255_D	271_V	0.693	1.00
272_S	278_T	0.693	1.00
148_I	183_I	0.692	1.00
178_L	286_L	0.690	1.00
95_P	99_K	0.684	1.00
252_L	281_K	0.683	1.00
1_M	25_H	0.682	1.00
83_T	128_F	0.682	1.00
241_T	262_K	0.682	1.00
171_L	230_L	0.680	1.00
51_V	315_M	0.679	1.00
4_L	50_I	0.678	1.00
185_I	206_N	0.678	1.00
65_A	68_R	0.678	1.00
150_V	230_L	0.675	1.00
229_G	238_T	0.673	1.00
143_K	146_C	0.673	1.00
302_A	306_D	0.671	1.00
226_I	292_R	0.671	1.00
220_V	223_S	0.667	1.00
108_V	239_Q	0.667	1.00
184_R	205_R	0.665	1.00
167_R	230_L	0.663	1.00
241_T	251_L	0.661	1.00
47_P	76_I	0.661	1.00
23_A	312_A	0.661	1.00
266_G	284_Y	0.660	1.00
23_A	309_R	0.659	1.00
245_L	302_A	0.659	1.00
15_G	19_G	0.657	1.00
290_S	294_K	0.657	1.00
53_M	81_W	0.657	1.00
221_Y	240_R	0.654	1.00
241_T	253_T	0.653	1.00
285_Y	292_R	0.652	1.00
280_E	283_K	0.652	1.00
77_P	103_D	0.652	1.00
294_K	297_I	0.651	1.00
221_Y	244_I	0.650	1.00
317_E	321_S	0.650	1.00
170_S	278_T	0.650	1.00
127_D	311_R	0.649	1.00
142_A	184_R	0.649	1.00
263_F	268_D	0.648	1.00
174_L	275_P	0.647	1.00
245_L	296_Q	0.647	1.00
269_L	272_S	0.647	1.00
272_S	277_E	0.645	1.00
35_R	39_T	0.644	1.00
299_G	302_A	0.643	1.00
219_K	222_S	0.641	1.00
178_L	279_L	0.638	1.00
288_H	292_R	0.638	1.00
127_D	314_R	0.637	1.00
32_P	36_E	0.636	1.00
240_R	244_I	0.634	1.00
115_T	119_M	0.632	1.00
52_S	58_E	0.629	1.00
12_W	315_M	0.628	1.00
127_D	306_D	0.628	1.00
307_S	311_R	0.627	1.00
172_K	206_N	0.626	1.00
225_K	292_R	0.622	1.00
146_C	149_A	0.622	1.00
214_Y	218_Y	0.620	1.00
199_I	202_E	0.620	1.00
152_A	168_S	0.618	1.00
15_G	131_H	0.617	1.00
245_L	268_D	0.617	1.00
156_P	193_E	0.616	1.00
318_V	321_S	0.615	1.00
221_Y	227_I	0.614	1.00
110_P	127_D	0.614	1.00
252_L	282_V	0.614	1.00
242_Y	306_D	0.613	1.00
315_M	319_L	0.612	1.00
300_K	303_V	0.611	1.00
5_F	51_V	0.608	1.00
181_K	280_E	0.608	1.00
94_I	98_K	0.606	1.00
91_N	94_I	0.606	1.00
117_E	120_G	0.605	1.00
154_A	194_K	0.604	1.00
309_R	313_E	0.604	1.00
173_T	204_P	0.602	1.00
11_M	214_Y	0.602	1.00
173_T	177_P	0.602	1.00
43_D	74_V	0.601	1.00
252_L	272_S	0.599	1.00
50_I	76_I	0.596	1.00
284_Y	287_N	0.592	1.00
49_L	79_V	0.592	1.00
4_L	28_M	0.590	1.00
221_Y	249_G	0.588	1.00
318_V	322_R	0.587	1.00
228_I	278_T	0.586	1.00
40_E	44_E	0.586	1.00
242_Y	303_V	0.585	1.00
268_D	298_N	0.583	1.00
169_S	196_S	0.582	1.00
308_Y	312_A	0.582	1.00
265_P	270_I	0.581	1.00
12_W	81_W	0.578	1.00
182_G	205_R	0.572	1.00
154_A	191_N	0.571	1.00
265_P	268_D	0.570	1.00
71_T	74_V	0.568	1.00
13_L	29_I	0.568	1.00
74_V	77_P	0.566	1.00
290_S	293_K	0.564	1.00
112_L	236_Q	0.562	1.00
151_V	227_I	0.561	1.00
117_E	123_A	0.560	1.00
276_K	279_L	0.557	1.00
17_P	27_V	0.557	1.00
50_I	71_T	0.556	1.00
149_A	249_G	0.554	1.00
250_F	299_G	0.554	1.00
226_I	252_L	0.551	1.00
252_L	285_Y	0.549	1.00
146_C	292_R	0.548	1.00
111_S	114_K	0.547	1.00
49_L	323_G	0.547	1.00
174_L	282_V	0.547	1.00
181_K	279_L	0.545	1.00
158_F	235_S	0.544	1.00
90_Q	94_I	0.544	1.00
33_V	37_N	0.543	1.00
25_H	320_K	0.542	1.00
82_A	112_L	0.541	1.00
156_P	169_S	0.541	1.00
152_A	158_F	0.539	1.00
22_E	309_R	0.537	1.00
83_T	108_V	0.536	1.00
305_N	310_H	0.536	1.00
11_M	14_Y	0.535	1.00
8_S	56_T	0.534	1.00
305_N	314_R	0.534	1.00
109_T	112_L	0.534	1.00
219_K	223_S	0.533	1.00
12_W	16_L	0.532	1.00
158_F	240_R	0.532	1.00
132_E	246_G	0.530	1.00
212_L	217_A	0.530	1.00
244_I	251_L	0.529	1.00
263_F	271_V	0.526	1.00
237_L	306_D	0.525	1.00
260_R	271_V	0.523	1.00
81_W	106_F	0.522	1.00
298_N	302_A	0.521	1.00
144_Y	182_G	0.521	1.00
169_S	232_N	0.519	1.00
54_G	57_P	0.518	1.00
19_G	308_Y	0.518	1.00
81_W	319_L	0.517	1.00
175_I	178_L	0.517	1.00
28_M	41_M	0.516	1.00
111_S	260_R	0.516	1.00
197_K	208_I	0.515	1.00
176_R	203_I	0.515	1.00
8_S	54_G	0.514	1.00
30_S	41_M	0.513	1.00
135_H	246_G	0.513	1.00
12_W	53_M	0.513	1.00
15_G	239_Q	0.508	1.00
150_V	185_I	0.508	1.00
158_F	231_Q	0.506	1.00
84_E	157_N	0.505	1.00
21_R	25_H	0.504	1.00
84_E	87_L	0.503	1.00
231_Q	240_R	0.503	1.00
95_P	98_K	0.503	1.00
153_N	158_F	0.502	1.00
226_I	286_L	0.501	1.00
12_W	108_V	0.500	1.00
179_I	183_I	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
2r60A	1	0.7719	100	0.424	Contact Map
4n9wA	1	0.7544	100	0.426	Contact Map
1rzuA	1	0.7719	100	0.43	Contact Map
2qzsA	1	0.7619	100	0.431	Contact Map
3c48A	2	0.787	100	0.442	Contact Map
3froA	3	0.7845	100	0.443	Contact Map
3oy2A	2	0.7769	100	0.457	Contact Map
2x6qA	1	0.7544	100	0.459	Contact Map
2x0dA	2	0.7243	100	0.463	Contact Map
3okpA	1	0.7619	100	0.463	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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