INTQ - ECOLI - GREMLIN Contacts

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INTQ - Putative lambdoid prophage Qin defective integrase (Fragment)

UniProt:	P76168	Sequences: GELRSSVCYAIKTGVFDYAKQFPSSRNLEKFGEARQDLTIKELAEKFLALKETEVAKTSLNTYRAVIKNILSIIGEKNLASSINKEKLLEVRKELLTGYQIPKSNYIVTQPGRSAVTVNNYMTNLNAVFQFGVDNGYLADNPFKGISPLKESRTIPDPLSREEFIRLIDACRNQQAKNLWCVSVYTGVRPGELCALGWEDIDLKNGTMMIRRNLAKDRFTVPKTQAGTNRVIHLIKPAIDALRSQMTLTRLSKEHIIDVHFREYGRTEKQKCTFVFQPEVSARVKNYGDHFTVDSIRQMWDAAIKRAGLRHRKSYQSRHTYACWSLTAGANPAFIANQMGHADAQMVFQVYGKWMSENNNAQVALLNTQLSEFAPTMPHNEAMKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13188
Length:	385 (300)
Sequences:	18569 (15390)
Seq/√Len:	888.5

ECOLI - INTQ INTR INTD INTF INTA INTZ INTB INTS XERC XERD INTE FIME FIMB
BACSU - INT YOMM XERC YOPP XERD YOEC
HALSA - Q9HR66 Q9HQV5 Q9HSI7 O52010 O54590
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
322_A	339_M	4.785	1.00
198_W	246_M	3.256	1.00
84_N	87_K	3.220	1.00
77_K	87_K	2.875	1.00
313_K	316_Q	2.770	1.00
206_G	239_I	2.743	1.00
187_G	321_Y	2.732	1.00
230_R	340_G	2.731	1.00
321_Y	338_Q	2.664	1.00
183_S	314_S	2.527	1.00
209_M	231_V	2.475	1.00
190_P	315_Y	2.339	1.00
95_L	121_Y	2.321	1.00
41_K	71_L	2.229	1.00
178_N	245_Q	2.223	1.00
44_A	67_I	2.217	1.00
207_T	231_V	2.184	1.00
73_I	94_E	2.171	1.00
183_S	193_L	2.156	1.00
319_H	353_K	2.140	1.00
202_D	205_N	2.109	1.00
92_R	122_M	2.088	1.00
197_G	273_T	2.056	1.00
64_R	68_K	2.019	1.00
239_I	243_R	1.958	1.00
131_F	135_N	1.952	1.00
331_N	334_F	1.942	1.00
44_A	128_V	1.923	1.00
321_Y	325_S	1.909	1.00
185_Y	235_I	1.850	1.00
332_P	348_F	1.830	1.00
188_V	193_L	1.814	1.00
66_V	124_N	1.776	1.00
88_L	143_F	1.755	1.00
43_L	132_G	1.749	1.00
160_S	163_E	1.743	1.00
41_K	45_E	1.740	1.00
198_W	275_V	1.730	1.00
116_V	120_N	1.729	1.00
48_L	64_R	1.721	1.00
326_L	335_I	1.715	1.00
345_Q	349_Q	1.705	1.00
326_L	352_G	1.704	1.00
29_E	32_G	1.686	1.00
164_F	184_V	1.676	1.00
228_T	342_A	1.653	1.00
59_S	63_Y	1.643	1.00
45_E	71_L	1.637	1.00
56_A	221_V	1.635	1.00
233_H	338_Q	1.630	1.00
136_G	140_D	1.605	1.00
197_G	274_F	1.571	1.00
179_L	296_I	1.566	1.00
200_D	211_R	1.549	1.00
24_S	27_N	1.546	1.00
130_Q	144_K	1.533	1.00
190_P	194_C	1.528	1.00
43_L	131_F	1.524	1.00
83_I	129_F	1.522	1.00
178_N	244_S	1.513	1.00
343_D	349_Q	1.509	1.00
203_L	243_R	1.492	1.00
206_G	236_K	1.482	1.00
163_E	166_R	1.467	1.00
234_L	239_I	1.461	1.00
341_H	347_V	1.452	1.00
39_T	42_E	1.450	1.00
177_K	181_C	1.412	1.00
346_M	350_V	1.408	1.00
333_A	336_A	1.406	1.00
48_L	60_L	1.382	1.00
179_L	193_L	1.376	1.00
41_K	76_E	1.374	1.00
333_A	337_N	1.373	1.00
330_A	365_L	1.373	1.00
178_N	241_A	1.360	1.00
184_V	317_S	1.357	1.00
202_D	207_T	1.348	1.00
325_S	330_A	1.343	1.00
128_V	132_G	1.336	1.00
69_N	121_Y	1.335	1.00
159_L	312_R	1.322	1.00
325_S	335_I	1.313	1.00
327_T	358_N	1.313	1.00
196_L	208_M	1.308	1.00
159_L	320_T	1.303	1.00
197_G	200_D	1.303	1.00
78_N	82_S	1.297	1.00
122_M	126_N	1.292	1.00
185_Y	238_A	1.292	1.00
199_E	273_T	1.291	1.00
188_V	210_I	1.285	1.00
181_C	241_A	1.285	1.00
89_L	135_N	1.284	1.00
322_A	335_I	1.283	1.00
21_Q	25_S	1.280	1.00
164_F	324_W	1.278	1.00
192_E	230_R	1.276	1.00
336_A	344_A	1.272	1.00
297_R	301_D	1.267	1.00
62_T	65_A	1.266	1.00
52_E	60_L	1.254	1.00
133_V	138_L	1.247	1.00
166_R	170_A	1.233	1.00
46_K	50_L	1.222	1.00
43_L	79_L	1.212	1.00
159_L	167_L	1.207	1.00
161_R	324_W	1.201	1.00
126_N	130_Q	1.200	1.00
56_A	220_T	1.198	1.00
334_F	362_Q	1.194	1.00
91_V	121_Y	1.179	1.00
176_A	299_M	1.178	1.00
196_L	201_I	1.176	1.00
21_Q	24_S	1.172	1.00
91_V	95_L	1.167	1.00
134_D	147_S	1.162	1.00
68_K	71_L	1.156	1.00
69_N	72_S	1.154	1.00
339_M	347_V	1.154	1.00
236_K	240_D	1.153	1.00
237_P	367_N	1.153	1.00
337_N	359_N	1.152	1.00
96_L	118_V	1.148	1.00
224_T	228_T	1.141	1.00
234_L	238_A	1.137	1.00
172_R	177_K	1.130	1.00
74_I	91_V	1.123	1.00
26_R	29_E	1.111	1.00
66_V	120_N	1.107	1.00
361_A	365_L	1.104	1.00
245_Q	249_T	1.102	1.00
236_K	364_A	1.102	1.00
85_K	134_D	1.101	1.00
182_V	238_A	1.100	1.00
63_Y	124_N	1.099	1.00
37_D	81_S	1.086	1.00
301_D	311_H	1.086	1.00
67_I	71_L	1.080	1.00
40_I	128_V	1.078	1.00
235_I	238_A	1.075	1.00
299_M	302_A	1.072	1.00
130_Q	141_N	1.070	1.00
57_K	61_N	1.066	1.00
330_A	362_Q	1.066	1.00
61_N	65_A	1.066	1.00
168_I	181_C	1.065	1.00
179_L	276_F	1.064	1.00
274_F	290_H	1.063	1.00
343_D	346_M	1.062	1.00
55_V	63_Y	1.060	1.00
134_D	145_G	1.058	1.00
55_V	60_L	1.050	1.00
165_I	169_D	1.049	1.00
300_W	304_I	1.046	1.00
56_A	59_S	1.044	1.00
23_P	27_N	1.043	1.00
323_C	353_K	1.034	1.00
197_G	290_H	1.034	1.00
89_L	93_K	1.034	1.00
129_F	142_P	1.030	1.00
320_T	324_W	1.028	1.00
120_N	123_T	1.015	1.00
60_L	64_R	1.015	1.00
129_F	138_L	1.011	1.00
129_F	143_F	1.003	1.00
364_A	368_T	1.002	1.00
336_A	347_V	1.000	1.00
24_S	28_L	0.998	1.00
25_S	29_E	0.994	1.00
324_W	327_T	0.991	1.00
182_V	208_M	0.988	1.00
358_N	361_A	0.987	1.00
58_T	61_N	0.971	1.00
92_R	96_L	0.970	1.00
21_Q	26_R	0.970	1.00
190_P	293_V	0.968	1.00
171_C	303_A	0.966	1.00
96_L	115_A	0.962	1.00
170_A	306_R	0.959	1.00
323_C	352_G	0.953	1.00
190_P	314_S	0.949	1.00
41_K	75_G	0.949	1.00
170_A	307_A	0.948	1.00
78_N	81_S	0.947	1.00
47_F	127_A	0.941	1.00
45_E	64_R	0.941	1.00
203_L	239_I	0.933	1.00
194_C	293_V	0.930	1.00
330_A	334_F	0.929	1.00
327_T	355_M	0.925	1.00
119_N	149_L	0.918	1.00
73_I	91_V	0.916	1.00
191_G	195_A	0.915	1.00
86_E	135_N	0.912	1.00
85_K	136_G	0.912	1.00
95_L	118_V	0.912	1.00
167_L	180_W	0.906	1.00
181_C	237_P	0.905	1.00
185_Y	237_P	0.904	1.00
114_S	117_T	0.904	1.00
199_E	272_C	0.900	1.00
182_V	276_F	0.900	1.00
222_P	229_N	0.894	1.00
62_T	66_V	0.893	1.00
344_A	348_F	0.890	1.00
233_H	360_N	0.889	1.00
133_V	145_G	0.884	1.00
338_Q	359_N	0.877	1.00
360_N	364_A	0.877	1.00
43_L	128_V	0.875	1.00
237_P	240_D	0.874	1.00
246_M	249_T	0.868	1.00
117_T	121_Y	0.868	1.00
322_A	352_G	0.866	1.00
88_L	125_L	0.865	1.00
158_P	320_T	0.863	1.00
301_D	305_K	0.860	1.00
90_E	94_E	0.851	1.00
321_Y	339_M	0.851	1.00
77_K	82_S	0.851	1.00
200_D	212_R	0.843	1.00
182_V	193_L	0.838	1.00
246_M	250_R	0.837	1.00
26_R	30_K	0.836	1.00
40_I	125_L	0.833	1.00
95_L	113_R	0.833	1.00
86_E	90_E	0.832	1.00
209_M	229_N	0.830	1.00
122_M	143_F	0.830	1.00
43_L	135_N	0.824	1.00
198_W	249_T	0.819	1.00
163_E	310_R	0.817	1.00
44_A	71_L	0.814	1.00
328_A	365_L	0.814	1.00
322_A	326_L	0.812	1.00
44_A	48_L	0.811	1.00
116_V	119_N	0.810	1.00
278_P	289_D	0.808	1.00
243_R	246_M	0.807	1.00
21_Q	29_E	0.806	1.00
208_M	212_R	0.805	1.00
37_D	78_N	0.804	1.00
113_R	117_T	0.803	1.00
161_R	165_I	0.801	1.00
133_V	140_D	0.799	1.00
235_I	367_N	0.798	1.00
161_R	327_T	0.798	1.00
211_R	229_N	0.797	1.00
238_A	241_A	0.796	1.00
46_K	137_Y	0.796	1.00
171_C	177_K	0.791	1.00
70_I	125_L	0.790	1.00
184_V	324_W	0.786	1.00
292_T	295_S	0.785	1.00
58_T	62_T	0.783	1.00
331_N	358_N	0.782	1.00
336_A	349_Q	0.781	1.00
45_E	49_A	0.779	1.00
196_L	275_V	0.777	1.00
38_L	137_Y	0.766	1.00
200_D	221_V	0.766	1.00
295_S	298_Q	0.761	1.00
300_W	317_S	0.757	1.00
136_G	145_G	0.757	1.00
319_H	350_V	0.754	1.00
133_V	141_N	0.752	1.00
298_Q	302_A	0.746	1.00
62_T	120_N	0.742	1.00
190_P	297_R	0.740	1.00
159_L	163_E	0.739	1.00
38_L	42_E	0.739	1.00
297_R	314_S	0.736	1.00
132_G	138_L	0.735	1.00
66_V	121_Y	0.734	1.00
47_F	131_F	0.728	1.00
172_R	181_C	0.724	1.00
186_T	232_I	0.723	1.00
73_I	90_E	0.722	1.00
188_V	208_M	0.721	1.00
167_L	300_W	0.721	1.00
38_L	46_K	0.721	1.00
326_L	355_M	0.720	1.00
119_N	123_T	0.717	1.00
83_I	88_L	0.713	1.00
70_I	75_G	0.713	1.00
40_I	83_I	0.711	1.00
87_K	90_E	0.707	1.00
322_A	347_V	0.707	1.00
166_R	169_D	0.705	1.00
208_M	234_L	0.705	1.00
184_V	320_T	0.705	1.00
122_M	146_I	0.704	1.00
180_W	317_S	0.703	1.00
126_N	143_F	0.700	1.00
51_K	55_V	0.698	1.00
201_I	242_L	0.696	1.00
177_K	241_A	0.692	1.00
40_I	44_A	0.692	1.00
141_N	144_K	0.692	1.00
294_D	297_R	0.691	1.00
50_L	93_K	0.691	1.00
312_R	316_Q	0.689	1.00
161_R	328_A	0.688	1.00
92_R	118_V	0.688	1.00
296_I	314_S	0.685	1.00
156_P	313_K	0.685	1.00
197_G	212_R	0.685	1.00
326_L	332_P	0.684	1.00
295_S	299_M	0.681	1.00
93_K	96_L	0.680	1.00
240_D	243_R	0.680	1.00
178_N	276_F	0.679	1.00
22_F	26_R	0.678	1.00
233_H	359_N	0.675	1.00
26_R	32_G	0.675	1.00
22_F	31_F	0.674	1.00
236_K	367_N	0.674	1.00
49_A	52_E	0.674	1.00
51_K	54_E	0.671	1.00
171_C	180_W	0.670	1.00
57_K	60_L	0.670	1.00
175_Q	245_Q	0.668	1.00
42_E	45_E	0.666	1.00
133_V	144_K	0.666	1.00
334_F	358_N	0.665	1.00
187_G	339_M	0.665	1.00
126_N	144_K	0.663	1.00
21_Q	28_L	0.660	1.00
113_R	118_V	0.658	1.00
244_S	247_T	0.658	1.00
85_K	89_L	0.658	1.00
357_E	361_A	0.652	1.00
79_L	129_F	0.649	1.00
304_I	312_R	0.646	1.00
67_I	128_V	0.645	1.00
362_Q	365_L	0.644	1.00
361_A	364_A	0.643	1.00
357_E	360_N	0.642	1.00
51_K	127_A	0.640	1.00
299_M	303_A	0.639	1.00
280_V	289_D	0.637	1.00
170_A	303_A	0.637	1.00
129_F	133_V	0.634	1.00
355_M	358_N	0.632	1.00
132_G	137_Y	0.630	1.00
84_N	139_A	0.630	1.00
133_V	139_A	0.629	1.00
198_W	242_L	0.628	1.00
274_F	277_Q	0.628	1.00
46_K	131_F	0.628	1.00
323_C	354_W	0.627	1.00
27_N	31_F	0.625	1.00
65_A	68_K	0.624	1.00
207_T	360_N	0.623	1.00
91_V	125_L	0.621	1.00
222_P	228_T	0.619	1.00
38_L	81_S	0.618	1.00
333_A	349_Q	0.613	1.00
152_S	225_Q	0.613	1.00
203_L	234_L	0.613	1.00
245_Q	248_L	0.612	1.00
326_L	333_A	0.609	1.00
43_L	137_Y	0.607	1.00
28_L	31_F	0.607	1.00
129_F	141_N	0.606	1.00
21_Q	31_F	0.606	1.00
332_P	344_A	0.604	1.00
157_D	316_Q	0.603	1.00
69_N	113_R	0.602	1.00
300_W	314_S	0.602	1.00
188_V	196_L	0.600	1.00
28_L	32_G	0.600	1.00
55_V	59_S	0.599	1.00
331_N	362_Q	0.597	1.00
278_P	281_S	0.597	1.00
182_V	242_L	0.593	1.00
22_F	25_S	0.591	1.00
175_Q	178_N	0.582	1.00
204_K	243_R	0.581	1.00
201_I	208_M	0.580	1.00
22_F	28_L	0.578	1.00
42_E	46_K	0.578	1.00
127_A	131_F	0.576	1.00
203_L	206_G	0.576	1.00
125_L	143_F	0.574	1.00
130_Q	133_V	0.574	1.00
210_I	222_P	0.573	1.00
293_V	297_R	0.571	1.00
63_Y	66_V	0.569	1.00
348_F	352_G	0.568	1.00
333_A	348_F	0.567	1.00
93_K	97_T	0.566	1.00
327_T	357_E	0.563	1.00
164_F	320_T	0.563	1.00
327_T	354_W	0.563	1.00
338_Q	363_V	0.562	1.00
69_N	95_L	0.559	1.00
86_E	136_G	0.558	1.00
23_P	26_R	0.558	1.00
25_S	28_L	0.557	1.00
67_I	124_N	0.557	1.00
241_A	244_S	0.556	1.00
26_R	31_F	0.552	1.00
243_R	247_T	0.549	1.00
301_D	304_I	0.548	1.00
224_T	340_G	0.546	1.00
302_A	306_R	0.545	1.00
304_I	307_A	0.542	1.00
180_W	300_W	0.541	1.00
115_A	119_N	0.541	1.00
303_A	307_A	0.541	1.00
188_V	192_E	0.540	1.00
202_D	209_M	0.540	1.00
336_A	346_M	0.538	1.00
130_Q	145_G	0.538	1.00
158_P	353_K	0.536	1.00
197_G	272_C	0.536	1.00
181_C	238_A	0.536	1.00
202_D	206_G	0.534	1.00
46_K	90_E	0.533	1.00
75_G	78_N	0.532	1.00
162_E	166_R	0.530	1.00
140_D	145_G	0.530	1.00
77_K	83_I	0.530	1.00
188_V	232_I	0.527	1.00
183_S	190_P	0.526	1.00
41_K	67_I	0.526	1.00
240_D	244_S	0.524	1.00
332_P	336_A	0.524	1.00
128_V	131_F	0.524	1.00
193_L	314_S	0.522	1.00
164_F	168_I	0.521	1.00
84_N	136_G	0.519	1.00
326_L	354_W	0.519	1.00
186_T	238_A	0.518	1.00
138_L	142_P	0.518	1.00
91_V	94_E	0.517	1.00
21_Q	27_N	0.516	1.00
364_A	367_N	0.516	1.00
69_N	112_G	0.516	1.00
38_L	43_L	0.512	1.00
330_A	335_I	0.510	1.00
157_D	310_R	0.510	1.00
178_N	238_A	0.504	1.00
74_I	83_I	0.503	1.00
23_P	29_E	0.503	1.00
67_I	70_I	0.502	1.00
298_Q	301_D	0.501	1.00
359_N	363_V	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	0.8	100	0.315	Contact Map
1a0pA	1	0.6753	100	0.315	Contact Map
2a3vA	3	0.787	100	0.329	Contact Map
1z19A	3	0.7169	100	0.333	Contact Map
4a8eA	2	0.6883	100	0.364	Contact Map
1xo0A	3	0.7532	100	0.379	Contact Map
3nkhA	2	0.5247	100	0.467	Contact Map
1ae9A	4	0.4312	100	0.559	Contact Map
1aihA	2	0.426	99.9	0.593	Contact Map
4e0gA	2	0.6831	99.9	0.617	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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