CAPA - BACSU - GREMLIN Contacts

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CAPA - PGA biosynthesis protein CapA

UniProt:	P96738	Sequences: MKKELSFHEKLLKLTKQQKKKTNKHVFIAIPIVFVLMFAFMWAGKAETPKVKTYSDDVLSASFVGDIMMGRYVEKVTEQKGADSIFQYVEPIFRASDYVAGNFENPVTYQKNYKQADKEIHLQTNKESVKVLKDMNFTVLNSANNHAMDYGVQGMKDTLGEFAKQNLDIVGAGYSLSDAKKKISYQKVNGVTIATLGFTDVSGKGFAAKKNTPGVLPADPEIFIPMISEAKKHADIVVVQSHWGQEYDNDPNDRQRQLARAMSDAGADIIVGHHPHVLEPIEVYNGTVIFYSLGNFVFDQGWTRTRDSALVQYHLKKNGTGRFEVTPIDIHEATPAPVKKDSLKQKTIIRELTKDSNFAWKVEDGKLTFDIDHSDKLKSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	380 (303)
Sequences:	2241 (1785)
Seq/√Len:	102.6

BACSU - CAPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
163_A	169_I	3.992	1.00
263_S	287_T	3.697	1.00
194_A	230_A	3.515	1.00
64_V	101_G	3.334	1.00
275_P	292_S	3.294	1.00
194_A	234_A	3.070	1.00
142_S	172_A	3.030	1.00
290_F	311_V	2.762	1.00
62_S	96_S	2.733	1.00
93_F	99_V	2.709	1.00
198_F	226_M	2.556	1.00
239_V	267_A	2.530	1.00
240_Q	273_H	2.514	1.00
67_I	101_G	2.501	1.00
284_Y	289_I	2.457	1.00
269_I	313_Y	2.396	1.00
230_A	234_A	2.353	1.00
174_Y	178_D	2.325	1.00
243_W	259_A	2.312	1.00
63_F	271_V	2.307	1.00
108_T	157_D	2.268	1.00
101_G	137_F	2.250	1.00
260_R	264_D	2.229	1.00
308_S	328_I	2.182	1.00
141_N	197_G	2.182	1.00
61_A	238_V	2.176	1.00
264_D	284_Y	2.173	1.00
261_A	265_A	2.087	1.00
338_V	346_K	2.066	1.00
220_P	261_A	2.066	1.00
60_S	314_H	2.043	1.00
259_A	289_I	1.995	1.00
187_K	192_T	1.986	1.00
102_N	144_N	1.982	1.00
278_L	309_A	1.968	1.00
64_V	296_F	1.963	1.00
231_K	237_V	1.961	1.00
260_R	282_E	1.937	1.00
99_V	138_T	1.932	1.00
268_D	287_T	1.930	1.00
103_F	162_F	1.923	1.00
101_G	140_L	1.898	1.00
194_A	237_V	1.829	1.00
234_A	237_V	1.827	1.00
100_A	240_Q	1.824	1.00
147_A	172_A	1.819	1.00
64_V	137_F	1.795	1.00
59_L	189_N	1.776	1.00
260_R	284_Y	1.775	1.00
163_A	174_Y	1.770	1.00
107_V	129_V	1.743	1.00
90_E	94_R	1.715	1.00
108_T	154_G	1.701	1.00
60_S	312_Q	1.666	1.00
192_T	235_D	1.649	1.00
93_F	137_F	1.638	1.00
83_D	134_D	1.629	1.00
64_V	310_L	1.625	1.00
236_I	269_I	1.622	1.00
129_V	161_E	1.621	1.00
170_V	197_G	1.620	1.00
139_V	195_T	1.618	1.00
227_I	262_M	1.568	1.00
185_Y	234_A	1.566	1.00
104_E	145_N	1.564	1.00
241_S	262_M	1.557	1.00
176_L	180_K	1.543	1.00
96_S	99_V	1.532	1.00
224_I	228_S	1.509	1.00
62_S	310_L	1.489	1.00
175_S	178_D	1.489	1.00
185_Y	192_T	1.481	1.00
245_Q	252_N	1.471	1.00
198_F	223_F	1.469	1.00
130_K	165_Q	1.468	1.00
62_S	312_Q	1.460	1.00
260_R	289_I	1.459	1.00
129_V	165_Q	1.455	1.00
96_S	138_T	1.453	1.00
263_S	284_Y	1.445	1.00
162_F	167_L	1.444	1.00
263_S	289_I	1.441	1.00
137_F	140_L	1.441	1.00
243_W	255_Q	1.439	1.00
264_D	285_N	1.427	1.00
62_S	99_V	1.416	1.00
145_N	276_H	1.410	1.00
152_V	156_K	1.394	1.00
197_G	240_Q	1.390	1.00
141_N	240_Q	1.386	1.00
100_A	195_T	1.362	0.99
236_I	315_L	1.361	0.99
249_N	304_R	1.348	0.99
139_V	170_V	1.345	0.99
312_Q	324_E	1.343	0.99
309_A	325_V	1.336	0.99
131_V	135_M	1.331	0.99
283_V	288_V	1.331	0.99
168_D	186_Q	1.327	0.99
105_N	124_T	1.326	0.99
148_M	155_M	1.326	0.99
160_G	174_Y	1.319	0.99
59_L	193_I	1.313	0.99
159_L	169_I	1.297	0.99
100_A	139_V	1.294	0.99
312_Q	326_T	1.281	0.99
185_Y	194_A	1.281	0.99
185_Y	230_A	1.278	0.99
256_R	260_R	1.277	0.99
224_I	265_A	1.256	0.99
129_V	162_F	1.253	0.99
71_R	299_D	1.244	0.99
316_K	321_G	1.237	0.99
246_E	274_H	1.236	0.99
160_G	164_K	1.234	0.99
227_I	265_A	1.226	0.99
230_A	237_V	1.216	0.99
59_L	191_V	1.213	0.99
227_I	237_V	1.207	0.99
99_V	137_F	1.200	0.99
196_L	226_M	1.190	0.99
243_W	272_G	1.185	0.99
253_D	257_Q	1.185	0.99
59_L	188_V	1.180	0.98
109_Y	126_K	1.169	0.98
293_L	311_V	1.162	0.98
278_L	308_S	1.144	0.98
126_K	157_D	1.143	0.98
156_K	174_Y	1.139	0.98
89_V	296_F	1.122	0.98
145_N	242_H	1.120	0.98
104_E	242_H	1.113	0.98
92_I	310_L	1.106	0.98
185_Y	233_H	1.103	0.98
122_L	246_E	1.094	0.98
173_G	179_A	1.089	0.97
104_E	276_H	1.088	0.97
262_M	270_I	1.080	0.97
247_Y	305_T	1.070	0.97
185_Y	229_E	1.066	0.97
63_F	240_Q	1.060	0.97
144_N	242_H	1.055	0.97
106_P	150_Y	1.041	0.97
251_P	280_P	1.040	0.97
157_D	161_E	1.036	0.97
66_D	276_H	1.024	0.96
47_E	51_V	1.020	0.96
247_Y	300_Q	1.008	0.96
282_E	291_Y	1.006	0.96
199_T	202_S	1.006	0.96
108_T	123_Q	1.005	0.96
282_E	289_I	0.995	0.96
231_K	268_D	0.992	0.96
100_A	141_N	0.989	0.95
146_H	149_D	0.989	0.95
66_D	242_H	0.987	0.95
187_K	190_G	0.983	0.95
273_H	293_L	0.975	0.95
191_V	317_K	0.953	0.94
227_I	267_A	0.949	0.94
263_S	285_N	0.946	0.94
238_V	269_I	0.936	0.94
162_F	169_I	0.934	0.94
142_S	147_A	0.933	0.94
195_T	240_Q	0.929	0.94
288_V	313_Y	0.928	0.94
180_K	216_L	0.927	0.94
58_V	314_H	0.927	0.94
223_F	226_M	0.923	0.93
155_M	172_A	0.921	0.93
159_L	174_Y	0.920	0.93
193_I	315_L	0.915	0.93
198_F	241_S	0.913	0.93
224_I	261_A	0.909	0.93
273_H	292_S	0.903	0.93
110_Q	157_D	0.898	0.93
295_N	300_Q	0.892	0.92
106_P	158_T	0.891	0.92
239_V	270_I	0.889	0.92
205_G	209_K	0.889	0.92
257_Q	261_A	0.888	0.92
89_V	310_L	0.886	0.92
269_I	315_L	0.885	0.92
66_D	145_N	0.884	0.92
342_S	345_Q	0.884	0.92
161_E	164_K	0.882	0.92
102_N	242_H	0.879	0.92
67_I	132_L	0.872	0.91
123_Q	150_Y	0.867	0.91
142_S	169_I	0.863	0.91
239_V	262_M	0.862	0.91
66_D	102_N	0.862	0.91
290_F	293_L	0.856	0.91
220_P	258_L	0.854	0.91
69_M	128_S	0.854	0.91
264_D	289_I	0.849	0.90
220_P	257_Q	0.848	0.90
229_E	233_H	0.847	0.90
242_H	274_H	0.843	0.90
269_I	288_V	0.843	0.90
243_W	279_E	0.841	0.90
340_K	343_L	0.837	0.90
252_N	255_Q	0.834	0.89
170_V	195_T	0.829	0.89
255_Q	279_E	0.828	0.89
276_H	295_N	0.822	0.89
70_G	119_E	0.822	0.89
67_I	86_F	0.817	0.89
58_V	316_K	0.812	0.88
195_T	238_V	0.809	0.88
196_L	239_V	0.808	0.88
91_P	94_R	0.806	0.88
334_T	338_V	0.803	0.88
256_R	282_E	0.801	0.88
270_I	287_T	0.798	0.87
182_K	230_A	0.797	0.87
213_P	216_L	0.793	0.87
99_V	136_N	0.792	0.87
175_S	214_G	0.792	0.87
62_S	93_F	0.792	0.87
109_Y	157_D	0.791	0.87
87_Q	90_E	0.788	0.87
70_G	122_L	0.786	0.87
155_M	173_G	0.782	0.86
221_E	225_P	0.775	0.86
49_P	52_K	0.769	0.85
152_V	212_T	0.767	0.85
302_W	305_T	0.764	0.85
72_Y	299_D	0.763	0.85
223_F	262_M	0.759	0.85
133_K	167_L	0.756	0.84
146_H	276_H	0.755	0.84
46_A	50_K	0.753	0.84
321_G	327_P	0.748	0.84
69_M	73_V	0.748	0.84
244_G	274_H	0.747	0.84
251_P	279_E	0.747	0.84
259_A	291_Y	0.746	0.84
139_V	183_I	0.745	0.83
198_F	239_V	0.744	0.83
242_H	276_H	0.743	0.83
98_Y	186_Q	0.740	0.83
145_N	295_N	0.740	0.83
259_A	270_I	0.734	0.83
104_E	146_H	0.734	0.83
96_S	312_Q	0.733	0.82
182_K	194_A	0.731	0.82
106_P	154_G	0.729	0.82
183_I	186_Q	0.727	0.82
263_S	282_E	0.725	0.82
47_E	52_K	0.724	0.82
344_K	347_T	0.723	0.82
107_V	167_L	0.723	0.82
122_L	277_V	0.722	0.82
68_M	73_V	0.721	0.81
45_K	48_T	0.716	0.81
259_A	272_G	0.716	0.81
146_H	242_H	0.716	0.81
202_S	206_F	0.715	0.81
262_M	267_A	0.713	0.81
142_S	158_T	0.711	0.81
70_G	120_I	0.711	0.81
243_W	262_M	0.703	0.80
307_D	345_Q	0.701	0.80
212_T	217_P	0.701	0.80
267_A	287_T	0.698	0.79
331_H	336_A	0.692	0.79
214_G	217_P	0.692	0.79
275_P	279_E	0.692	0.79
199_T	215_V	0.691	0.79
88_Y	91_P	0.690	0.79
59_L	315_L	0.689	0.78
141_N	170_V	0.688	0.78
47_E	50_K	0.687	0.78
247_Y	295_N	0.687	0.78
66_D	104_E	0.687	0.78
48_T	52_K	0.685	0.78
45_K	53_T	0.682	0.78
260_R	263_S	0.682	0.78
70_G	300_Q	0.681	0.78
246_E	295_N	0.680	0.78
77_T	85_I	0.680	0.78
48_T	54_Y	0.673	0.77
85_I	297_V	0.672	0.77
105_N	144_N	0.670	0.76
200_D	254_R	0.670	0.76
92_I	95_A	0.669	0.76
180_K	226_M	0.667	0.76
48_T	51_V	0.662	0.76
227_I	231_K	0.662	0.76
120_I	300_Q	0.661	0.76
122_L	276_H	0.660	0.75
226_M	229_E	0.657	0.75
154_G	158_T	0.657	0.75
90_E	134_D	0.655	0.75
50_K	53_T	0.654	0.75
46_A	49_P	0.651	0.74
77_T	82_A	0.650	0.74
113_Y	116_A	0.648	0.74
237_V	268_D	0.645	0.74
103_F	106_P	0.643	0.74
300_Q	305_T	0.639	0.73
142_S	162_F	0.637	0.73
196_L	230_A	0.637	0.73
53_T	56_D	0.636	0.73
161_E	165_Q	0.636	0.73
323_F	327_P	0.635	0.73
277_V	292_S	0.635	0.73
98_Y	188_V	0.635	0.73
49_P	53_T	0.634	0.72
220_P	224_I	0.632	0.72
46_A	52_K	0.632	0.72
98_Y	139_V	0.630	0.72
126_K	164_K	0.630	0.72
104_E	274_H	0.630	0.72
122_L	145_N	0.629	0.72
93_F	96_S	0.627	0.72
192_T	233_H	0.626	0.72
109_Y	125_N	0.625	0.71
243_W	270_I	0.621	0.71
316_K	320_T	0.620	0.71
102_N	246_E	0.620	0.71
255_Q	272_G	0.619	0.71
248_D	279_E	0.617	0.70
68_M	71_R	0.614	0.70
164_K	232_K	0.614	0.70
129_V	167_L	0.613	0.70
56_D	316_K	0.611	0.70
347_T	350_R	0.610	0.70
328_I	335_P	0.608	0.69
142_S	155_M	0.607	0.69
46_A	54_Y	0.606	0.69
61_A	313_Y	0.605	0.69
104_E	295_N	0.605	0.69
140_L	162_F	0.604	0.69
222_I	225_P	0.604	0.69
241_S	270_I	0.602	0.69
49_P	54_Y	0.602	0.69
310_L	328_I	0.598	0.68
45_K	52_K	0.596	0.68
175_S	211_N	0.596	0.68
103_F	107_V	0.596	0.68
144_N	246_E	0.594	0.68
103_F	132_L	0.594	0.68
274_H	298_F	0.591	0.67
121_H	206_F	0.591	0.67
211_N	214_G	0.590	0.67
102_N	275_P	0.589	0.67
247_Y	308_S	0.589	0.67
83_D	164_K	0.587	0.67
144_N	273_H	0.586	0.67
274_H	295_N	0.586	0.67
140_L	167_L	0.585	0.66
106_P	124_T	0.584	0.66
47_E	54_Y	0.583	0.66
226_M	230_A	0.583	0.66
168_D	183_I	0.580	0.66
153_Q	156_K	0.579	0.66
69_M	105_N	0.579	0.66
98_Y	138_T	0.578	0.65
177_S	232_K	0.577	0.65
314_H	322_R	0.577	0.65
134_D	177_S	0.577	0.65
100_A	197_G	0.572	0.65
290_F	323_F	0.571	0.65
46_A	53_T	0.571	0.65
170_V	173_G	0.569	0.64
48_T	53_T	0.568	0.64
73_V	85_I	0.568	0.64
180_K	222_I	0.566	0.64
236_I	268_D	0.566	0.64
141_N	242_H	0.565	0.64
74_E	82_A	0.565	0.64
274_H	293_L	0.563	0.63
245_Q	248_D	0.563	0.63
214_G	218_A	0.562	0.63
45_K	282_E	0.561	0.63
303_T	306_R	0.561	0.63
110_Q	123_Q	0.560	0.63
251_P	256_R	0.559	0.63
173_G	214_G	0.558	0.63
46_A	51_V	0.557	0.63
345_Q	348_I	0.557	0.63
225_P	228_S	0.557	0.63
234_A	267_A	0.556	0.62
117_D	120_I	0.555	0.62
325_V	329_D	0.555	0.62
68_M	144_N	0.555	0.62
148_M	202_S	0.554	0.62
340_K	345_Q	0.553	0.62
66_D	274_H	0.553	0.62
119_E	200_D	0.552	0.62
159_L	163_A	0.547	0.61
237_V	267_A	0.547	0.61
270_I	284_Y	0.546	0.61
253_D	256_R	0.546	0.61
278_L	293_L	0.545	0.61
246_E	277_V	0.544	0.61
187_K	193_I	0.543	0.61
45_K	54_Y	0.542	0.61
191_V	194_A	0.541	0.60
145_N	149_D	0.540	0.60
104_E	122_L	0.540	0.60
231_K	234_A	0.539	0.60
212_T	218_A	0.537	0.60
278_L	294_G	0.537	0.60
316_K	319_G	0.537	0.60
63_F	293_L	0.537	0.60
335_P	338_V	0.536	0.60
93_F	101_G	0.535	0.60
329_D	342_S	0.533	0.59
119_E	308_S	0.533	0.59
245_Q	254_R	0.532	0.59
89_V	328_I	0.531	0.59
45_K	50_K	0.529	0.59
68_M	298_F	0.528	0.59
45_K	51_V	0.527	0.58
66_D	146_H	0.526	0.58
194_A	233_H	0.526	0.58
68_M	122_L	0.526	0.58
170_V	240_Q	0.525	0.58
260_R	291_Y	0.522	0.58
71_R	75_K	0.521	0.58
337_P	341_D	0.521	0.58
68_M	297_V	0.521	0.58
295_N	298_F	0.520	0.57
57_D	317_K	0.519	0.57
145_N	274_H	0.518	0.57
175_S	209_K	0.518	0.57
158_T	162_F	0.517	0.57
288_V	323_F	0.517	0.57
204_K	207_A	0.517	0.57
170_V	183_I	0.515	0.57
150_Y	154_G	0.515	0.57
69_M	297_V	0.513	0.56
92_I	337_P	0.512	0.56
67_I	140_L	0.512	0.56
182_K	185_Y	0.511	0.56
69_M	132_L	0.510	0.56
343_L	349_I	0.510	0.56
164_K	322_R	0.510	0.56
281_I	290_F	0.509	0.56
278_L	346_K	0.508	0.56
107_V	128_S	0.507	0.56
122_L	125_N	0.507	0.56
128_S	131_V	0.506	0.55
148_M	206_F	0.506	0.55
98_Y	195_T	0.505	0.55
102_N	273_H	0.505	0.55
274_H	300_Q	0.502	0.55
273_H	281_I	0.502	0.55
255_Q	259_A	0.502	0.55
68_M	300_Q	0.500	0.55
246_E	276_H	0.500	0.55

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
1t70A	2	0.6395	100	0.726	Contact Map
2z06A	4	0.6263	100	0.732	Contact Map
4b2oA	4	0.6237	100	0.737	Contact Map
1t71A	2	0.7	99.9	0.763	Contact Map
3gveA	2	0.7421	99.9	0.768	Contact Map
3c9fA	2	0.7789	99.9	0.778	Contact Map
3jyfA	2	0.7711	99.9	0.779	Contact Map
4q7fA	1	0.7579	99.9	0.789	Contact Map
1hp1A	1	0.8026	99.9	0.791	Contact Map
2z1aA	1	0.7684	99.9	0.794	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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