INTB - ECOLI - GREMLIN Contacts

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INTB - Putative prophage P4 integrase

UniProt:	P39347	Sequences: MHLLVHPNGSKYWRLQYRYEGKQKMLALGVYPEITLADARVRRDEARKLLANGVDPGDKKKNDKVEQSKARTFKEVAIEWHGTNKKWSEDHAHRVLKSLEDNLFAALGERNIAELKTRDLLAPIKAVEMSGRLEVAARLQQRTTAIMRYAVQSGLIDYNPAQEMAGAVASCNRQHRPALELKRIPELLTKIDSYTGRPLTRWAIELTLLIFIRSSELRFARWSEIDFEASIWTIPPEREPIPGVKHSHRGSKMRTTHLVPLSTQALAILKQIKQFYGAHDLIFIGDHDSHKPMSENTVNSALRVMGYDTKVEVCGHGFRTMACSSLVESGLWSRDAVERQMSHMARNSVRAAYIHKAEHLEERRLMLQWWADFLDVNRERFISPFEYAKINNPLKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12364
Length:	396 (327)
Sequences:	19221 (16217)
Seq/√Len:	896.8

ECOLI - INTB INTA INTF INTZ INTS INTD INTR INTE INTQ XERC XERD FIME
BACSU - INT XERC YOPP YOMM XERD YOEC
HALSA - Q9HR66 Q9HQV5 Q9HSI7 O54590 O52010
SULSO - Q980D9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
323_C	341_M	4.765	1.00
110_R	119_D	3.310	1.00
222_W	273_K	3.181	1.00
314_C	317_G	2.865	1.00
116_K	119_D	2.864	1.00
257_H	342_S	2.782	1.00
214_S	316_H	2.737	1.00
207_T	315_G	2.721	1.00
252_K	255_T	2.685	1.00
322_A	340_Q	2.562	1.00
211_F	322_A	2.514	1.00
202_W	272_I	2.409	1.00
230_S	266_L	2.398	1.00
320_T	355_H	2.381	1.00
226_D	229_A	2.358	1.00
127_V	139_L	2.344	1.00
221_R	280_D	2.301	1.00
42_R	45_E	2.243	1.00
233_T	258_L	2.180	1.00
77_A	146_I	2.089	1.00
207_T	217_L	2.076	1.00
74_K	104_F	2.052	1.00
16_Q	23_Q	2.033	1.00
96_L	100_E	2.021	1.00
124_I	140_Q	2.017	1.00
77_A	99_L	1.980	1.00
322_A	326_L	1.966	1.00
231_I	258_L	1.950	1.00
36_L	40_R	1.948	1.00
106_A	126_A	1.905	1.00
76_V	150_A	1.882	1.00
334_R	350_R	1.877	1.00
327_V	337_V	1.856	1.00
74_K	78_I	1.850	1.00
78_I	104_F	1.840	1.00
222_W	282_I	1.832	1.00
260_P	340_Q	1.815	1.00
149_Y	153_S	1.790	1.00
76_V	112_I	1.757	1.00
120_L	161_A	1.749	1.00
134_E	138_R	1.747	1.00
154_G	158_Y	1.745	1.00
333_S	336_A	1.741	1.00
111_N	114_E	1.740	1.00
202_W	271_Q	1.731	1.00
148_R	162_Q	1.727	1.00
46_A	49_L	1.717	1.00
212_I	217_L	1.692	1.00
74_K	109_E	1.688	1.00
266_L	270_K	1.681	1.00
180_E	183_R	1.670	1.00
209_L	262_S	1.651	1.00
45_E	49_L	1.630	1.00
18_R	23_Q	1.622	1.00
81_H	96_L	1.613	1.00
98_S	142_R	1.590	1.00
327_V	354_I	1.560	1.00
42_R	46_A	1.550	1.00
35_T	38_D	1.548	1.00
230_S	263_T	1.524	1.00
76_V	149_Y	1.518	1.00
91_H	95_V	1.500	1.00
255_T	344_M	1.497	1.00
224_E	235_P	1.483	1.00
216_E	257_H	1.479	1.00
263_T	267_A	1.466	1.00
115_L	147_M	1.464	1.00
348_S	352_A	1.440	1.00
214_S	218_R	1.438	1.00
184_I	208_L	1.418	1.00
183_R	186_E	1.411	1.00
85_K	92_A	1.409	1.00
208_L	318_F	1.408	1.00
48_K	52_N	1.381	1.00
16_Q	25_M	1.375	1.00
345_A	348_S	1.373	1.00
140_Q	144_T	1.361	1.00
201_R	205_E	1.353	1.00
79_E	83_T	1.352	1.00
223_S	280_D	1.346	1.00
121_L	153_S	1.344	1.00
263_T	368_Q	1.343	1.00
345_A	351_A	1.342	1.00
302_L	306_G	1.340	1.00
221_R	281_L	1.335	1.00
212_I	234_I	1.334	1.00
220_A	225_I	1.331	1.00
202_W	268_I	1.328	1.00
323_C	337_V	1.327	1.00
81_H	92_A	1.303	1.00
72_T	75_E	1.301	1.00
326_L	332_W	1.299	1.00
203_A	217_L	1.297	1.00
117_T	152_Q	1.295	1.00
326_L	337_V	1.295	1.00
179_L	313_V	1.293	1.00
152_Q	165_A	1.292	1.00
336_A	366_M	1.287	1.00
184_I	325_S	1.283	1.00
299_N	303_R	1.282	1.00
335_D	338_E	1.276	1.00
227_F	270_K	1.268	1.00
179_L	187_L	1.266	1.00
220_A	232_W	1.266	1.00
261_L	265_A	1.261	1.00
226_D	231_I	1.260	1.00
146_I	150_A	1.251	1.00
97_K	101_D	1.249	1.00
92_A	96_L	1.239	1.00
43_R	47_R	1.222	1.00
192_D	201_R	1.221	1.00
110_R	114_E	1.219	1.00
121_L	125_K	1.217	1.00
203_A	298_V	1.217	1.00
99_L	104_F	1.211	1.00
151_V	156_I	1.201	1.00
224_E	238_R	1.199	1.00
144_T	148_R	1.198	1.00
78_I	82_G	1.196	1.00
332_W	369_W	1.194	1.00
261_L	266_L	1.191	1.00
107_L	123_P	1.188	1.00
206_L	265_A	1.185	1.00
324_S	354_I	1.170	1.00
186_E	190_K	1.170	1.00
45_E	48_K	1.167	1.00
44_D	51_A	1.162	1.00
85_K	96_L	1.162	1.00
179_L	321_M	1.159	1.00
94_R	97_K	1.155	1.00
343_H	349_V	1.145	1.00
87_W	95_V	1.143	1.00
152_Q	163_E	1.139	1.00
148_R	159_N	1.137	1.00
348_S	351_A	1.136	1.00
321_M	325_S	1.136	1.00
123_P	139_L	1.131	1.00
185_P	189_T	1.126	1.00
262_S	265_A	1.119	1.00
88_S	91_H	1.119	1.00
345_A	349_V	1.113	1.00
338_E	346_R	1.112	1.00
132_R	135_V	1.111	1.00
332_W	366_M	1.108	1.00
70_A	113_A	1.103	1.00
272_I	276_Y	1.101	1.00
181_L	325_S	1.098	1.00
95_V	142_R	1.085	1.00
349_V	352_A	1.085	1.00
89_E	93_H	1.081	1.00
12_Y	27_A	1.079	1.00
76_V	153_S	1.070	1.00
117_T	154_G	1.061	1.00
188_L	205_E	1.051	1.00
338_E	350_R	1.042	1.00
84_N	87_W	1.040	1.00
205_E	268_I	1.039	1.00
328_E	362_E	1.036	1.00
123_P	127_V	1.035	1.00
100_E	104_F	1.030	1.00
221_R	224_E	1.029	1.00
14_R	27_A	1.026	1.00
335_D	339_R	1.018	1.00
118_R	153_S	1.017	1.00
41_V	45_E	1.016	1.00
206_L	232_W	1.014	1.00
209_L	265_A	1.013	1.00
70_A	111_N	1.011	1.00
73_F	146_I	1.008	1.00
264_Q	267_A	1.007	1.00
40_R	44_D	1.006	1.00
178_A	321_M	1.003	1.00
37_A	41_V	1.001	1.00
365_L	369_W	0.995	1.00
324_S	355_H	0.989	1.00
74_K	108_G	0.987	1.00
214_S	315_G	0.984	1.00
328_E	359_H	0.984	1.00
49_L	54_V	0.983	1.00
205_E	264_Q	0.983	1.00
362_E	365_L	0.974	1.00
223_S	279_H	0.973	1.00
232_W	236_P	0.971	1.00
147_M	161_A	0.970	1.00
203_A	283_F	0.961	1.00
301_A	304_V	0.961	1.00
147_M	156_I	0.956	1.00
206_L	217_L	0.952	1.00
118_R	122_A	0.949	1.00
127_V	136_A	0.947	1.00
138_R	141_Q	0.945	1.00
147_M	160_P	0.945	1.00
303_R	312_E	0.944	1.00
15_L	42_R	0.943	1.00
78_I	96_L	0.942	1.00
47_R	51_A	0.942	1.00
325_S	328_E	0.940	1.00
140_Q	161_A	0.937	1.00
93_H	97_K	0.933	1.00
181_L	185_P	0.932	1.00
87_W	92_A	0.927	1.00
44_D	47_R	0.924	1.00
144_T	162_Q	0.918	1.00
270_K	273_K	0.913	1.00
224_E	236_P	0.913	1.00
48_K	51_A	0.912	1.00
37_A	40_R	0.908	1.00
364_R	368_Q	0.907	1.00
76_V	146_I	0.902	1.00
151_V	158_Y	0.901	1.00
200_T	301_A	0.897	1.00
134_E	137_A	0.887	1.00
151_V	163_E	0.884	1.00
73_F	77_A	0.883	1.00
120_L	143_T	0.880	1.00
191_I	204_I	0.879	1.00
41_V	44_D	0.879	1.00
338_E	351_A	0.878	1.00
41_V	51_A	0.876	1.00
190_K	309_T	0.876	1.00
209_L	264_Q	0.875	1.00
112_I	147_M	0.871	1.00
338_E	349_V	0.871	1.00
8_N	11_K	0.870	1.00
332_W	336_A	0.869	1.00
323_C	354_I	0.865	1.00
350_R	354_I	0.864	1.00
220_A	282_I	0.862	1.00
135_V	139_L	0.861	1.00
38_D	42_R	0.859	1.00
323_C	327_V	0.859	1.00
322_A	341_M	0.855	1.00
144_T	161_A	0.855	1.00
222_W	276_Y	0.855	1.00
329_S	369_W	0.854	1.00
45_E	52_N	0.853	1.00
13_W	36_L	0.853	1.00
121_L	124_I	0.851	1.00
339_R	363_R	0.846	1.00
346_R	351_A	0.843	1.00
71_R	155_L	0.842	1.00
90_D	93_H	0.839	1.00
89_E	92_A	0.837	1.00
227_F	266_L	0.836	1.00
219_F	238_R	0.835	1.00
323_C	350_R	0.833	1.00
192_D	205_E	0.833	1.00
217_L	315_G	0.829	1.00
71_R	75_E	0.829	1.00
260_P	363_R	0.828	1.00
94_R	98_S	0.827	1.00
84_N	145_A	0.826	1.00
122_A	126_A	0.825	1.00
300_S	304_V	0.824	1.00
215_S	219_F	0.823	1.00
116_K	154_G	0.822	1.00
265_A	268_I	0.822	1.00
273_K	276_Y	0.821	1.00
115_L	120_L	0.820	1.00
116_K	157_D	0.820	1.00
317_G	320_T	0.818	1.00
73_F	143_T	0.816	1.00
19_Y	24_K	0.815	1.00
97_K	100_E	0.815	1.00
49_L	52_N	0.814	1.00
77_A	81_H	0.812	1.00
359_H	362_E	0.811	1.00
151_V	159_N	0.810	1.00
147_M	151_V	0.806	1.00
183_R	311_V	0.805	1.00
112_I	150_A	0.802	1.00
44_D	48_K	0.800	1.00
222_W	269_L	0.800	1.00
28_L	42_R	0.799	1.00
187_L	204_I	0.799	1.00
297_T	300_S	0.798	1.00
214_S	295_E	0.798	1.00
177_P	183_R	0.797	1.00
273_K	277_G	0.795	1.00
313_V	317_G	0.794	1.00
204_I	318_F	0.791	1.00
190_K	308_D	0.789	1.00
159_N	162_Q	0.788	1.00
38_D	41_V	0.788	1.00
346_R	350_R	0.787	1.00
106_A	122_A	0.786	1.00
36_L	39_A	0.778	1.00
340_Q	363_R	0.778	1.00
73_F	115_L	0.778	1.00
177_P	311_V	0.771	1.00
320_T	352_A	0.770	1.00
323_C	349_V	0.768	1.00
191_I	201_R	0.766	1.00
343_H	350_R	0.766	1.00
90_D	94_R	0.763	1.00
341_M	350_R	0.758	1.00
80_W	145_A	0.758	1.00
119_D	122_A	0.757	1.00
71_R	79_E	0.756	1.00
80_W	84_N	0.754	1.00
118_R	154_G	0.754	1.00
285_G	291_K	0.753	1.00
206_L	283_F	0.749	1.00
361_E	364_R	0.748	1.00
333_S	362_E	0.747	1.00
176_R	314_C	0.746	1.00
103_L	143_T	0.743	1.00
81_H	85_K	0.737	1.00
327_V	335_D	0.737	1.00
79_E	155_L	0.736	1.00
53_G	56_P	0.731	1.00
260_P	364_R	0.729	1.00
208_L	321_M	0.728	1.00
227_F	261_L	0.726	1.00
137_A	169_A	0.726	1.00
77_A	104_F	0.725	1.00
12_Y	30_V	0.723	1.00
34_I	38_D	0.723	1.00
336_A	362_E	0.721	1.00
361_E	365_L	0.720	1.00
212_I	216_E	0.719	1.00
124_I	136_A	0.717	1.00
346_R	349_V	0.716	1.00
106_A	123_P	0.715	1.00
40_R	43_R	0.715	1.00
41_V	48_K	0.713	1.00
14_R	25_M	0.711	1.00
80_W	149_Y	0.711	1.00
323_C	338_E	0.710	1.00
327_V	334_R	0.708	1.00
213_R	236_P	0.704	1.00
360_L	363_R	0.702	1.00
198_P	201_R	0.701	1.00
94_R	138_R	0.699	1.00
39_A	43_R	0.696	1.00
72_T	111_N	0.695	1.00
267_A	270_K	0.693	1.00
225_I	269_L	0.691	1.00
179_L	183_R	0.691	1.00
340_Q	367_L	0.690	1.00
338_E	348_S	0.688	1.00
212_I	220_A	0.687	1.00
154_G	163_E	0.685	1.00
306_G	309_T	0.684	1.00
186_E	189_T	0.681	1.00
12_Y	34_I	0.680	1.00
124_I	128_E	0.679	1.00
212_I	232_W	0.679	1.00
225_I	232_W	0.678	1.00
117_T	163_E	0.677	1.00
221_R	236_P	0.677	1.00
151_V	162_Q	0.675	1.00
78_I	100_E	0.674	1.00
345_A	350_R	0.674	1.00
206_L	210_I	0.674	1.00
101_D	139_L	0.673	1.00
79_E	153_S	0.669	1.00
87_W	91_H	0.666	1.00
334_R	338_E	0.666	1.00
75_E	79_E	0.662	1.00
187_L	302_L	0.661	1.00
218_R	295_E	0.661	1.00
103_L	108_G	0.658	1.00
281_L	284_I	0.658	1.00
233_T	256_T	0.656	1.00
210_I	259_V	0.654	1.00
98_S	139_L	0.654	1.00
297_T	301_A	0.652	1.00
338_E	341_M	0.652	1.00
206_L	269_L	0.652	1.00
303_R	307_Y	0.648	1.00
214_S	299_N	0.647	1.00
107_L	119_D	0.646	1.00
83_T	125_K	0.646	1.00
150_A	156_I	0.645	1.00
329_S	332_W	0.645	1.00
366_M	369_W	0.644	1.00
146_I	149_Y	0.641	1.00
15_L	46_A	0.640	1.00
147_M	159_N	0.640	1.00
17_Y	24_K	0.637	1.00
338_E	345_A	0.636	1.00
128_E	136_A	0.636	1.00
101_D	105_A	0.636	1.00
178_A	324_S	0.635	1.00
235_P	256_T	0.634	1.00
365_L	368_Q	0.634	1.00
125_K	153_S	0.633	1.00
121_L	152_Q	0.633	1.00
299_N	315_G	0.632	1.00
76_V	155_L	0.632	1.00
296_N	300_S	0.631	1.00
79_E	122_A	0.629	1.00
226_D	230_S	0.629	1.00
117_T	121_L	0.629	1.00
213_R	316_H	0.624	1.00
137_A	141_Q	0.624	1.00
140_Q	164_M	0.623	1.00
335_D	350_R	0.622	1.00
75_E	78_I	0.620	1.00
188_L	209_L	0.620	1.00
84_N	95_V	0.619	1.00
211_F	341_M	0.619	1.00
156_I	160_P	0.619	1.00
328_E	361_E	0.617	1.00
210_I	262_S	0.617	1.00
128_E	131_G	0.615	1.00
95_V	98_S	0.615	1.00
326_L	340_Q	0.614	1.00
335_D	351_A	0.613	1.00
181_L	329_S	0.613	1.00
360_L	364_R	0.610	1.00
190_K	305_M	0.609	1.00
55_D	58_D	0.609	1.00
79_E	82_G	0.609	1.00
15_L	43_R	0.607	1.00
334_R	351_A	0.607	1.00
287_H	291_K	0.605	1.00
208_L	325_S	0.604	1.00
79_E	149_Y	0.602	1.00
145_A	149_Y	0.601	1.00
71_R	113_A	0.601	1.00
82_G	85_K	0.600	1.00
327_V	350_R	0.598	1.00
316_H	341_M	0.598	1.00
104_F	108_G	0.598	1.00
27_A	30_V	0.597	1.00
184_I	321_M	0.596	1.00
298_V	315_G	0.595	1.00
227_F	230_S	0.591	1.00
74_K	99_L	0.590	1.00
232_W	261_L	0.588	1.00
107_L	115_L	0.587	1.00
268_I	271_Q	0.586	1.00
210_I	265_A	0.586	1.00
231_I	364_R	0.585	1.00
15_L	28_L	0.580	1.00
91_H	94_R	0.573	1.00
221_R	238_R	0.572	1.00
271_Q	274_Q	0.571	1.00
99_L	146_I	0.570	1.00
148_R	152_Q	0.567	1.00
298_V	302_L	0.567	1.00
296_N	299_N	0.567	1.00
212_I	259_V	0.564	1.00
188_L	201_R	0.564	1.00
252_K	256_T	0.562	1.00
123_P	126_A	0.558	1.00
227_F	232_W	0.557	1.00
301_A	305_M	0.556	1.00
198_P	271_Q	0.555	1.00
323_C	343_H	0.555	1.00
50_L	55_D	0.552	1.00
210_I	217_L	0.552	1.00
332_W	337_V	0.552	1.00
110_R	115_L	0.551	1.00
181_L	328_E	0.550	1.00
148_R	151_V	0.545	1.00
26_L	46_A	0.544	1.00
182_K	185_P	0.543	1.00
204_I	302_L	0.540	1.00
281_L	292_P	0.538	1.00
198_P	202_W	0.537	1.00
299_N	302_L	0.536	1.00
177_P	317_G	0.535	1.00
190_K	193_S	0.534	1.00
99_L	103_L	0.534	1.00
334_R	346_R	0.530	1.00
117_T	153_S	0.529	1.00
133_L	137_A	0.528	1.00
260_P	367_L	0.527	1.00
333_S	366_M	0.527	1.00
302_L	318_F	0.523	1.00
125_K	128_E	0.521	1.00
363_R	367_L	0.520	1.00
83_T	149_Y	0.519	1.00
267_A	271_Q	0.516	1.00
254_R	344_M	0.516	1.00
253_M	342_S	0.516	1.00
152_Q	162_Q	0.516	1.00
47_R	50_L	0.514	1.00
15_L	50_L	0.511	1.00
228_E	270_K	0.511	1.00
143_T	161_A	0.511	1.00
103_L	123_P	0.508	1.00
306_G	312_E	0.504	1.00
173_R	253_M	0.501	1.00
304_V	308_D	0.501	1.00
121_L	164_M	0.500	1.00
30_V	35_T	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
1z1bA	3	0.8359	100	0.297	Contact Map
1a0pA	1	0.6439	100	0.356	Contact Map
1z19A	3	0.6818	100	0.364	Contact Map
2a3vA	3	0.6944	100	0.366	Contact Map
4a8eA	2	0.6591	100	0.405	Contact Map
1xo0A	3	0.7197	100	0.408	Contact Map
3nkhA	2	0.5	100	0.51	Contact Map
1ae9A	4	0.404	100	0.585	Contact Map
1aihA	2	0.4293	99.9	0.608	Contact Map
4e0gA	2	0.6667	99.9	0.63	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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