LPSRP - ECOLI - GREMLIN Contacts

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LPSRP - Lipopolysaccharide regulatory protein

UniProt:	P0AB58	Sequences: MLELLFLLLPVAAAYGWYMGRRSAQQNKQDEANRLSRDYVAGVNFLLSNQQDKAVDLFLDMLKEDTGTVEAHLTLGNLFRSRGEVDRAIRIHQTLMESASLTYEQRLLAIQQLGRDYMAAGLYDRAEDMFNQLTDETDFRIGALQQLLQIYQATSEWQKAIDVAERLVKLGKDKQRVEIAHFYCELALQHMASDDLDRAMTLLKKGAAADKNSARVSIMMGRVFMAKGEYAKAVESLQRVISQDRELVSETLEMLQTCYQQLGKTAEWAEFLQRAVEENTGADAELMLADIIEARDGSEAAQVYITRQLQRHPTMRVFHKLMDYHLNEAEEGRAKESLMVLRDMVGEKVRSKPRYRCQKCGFTAYTLYWHCPSCRAWSTIKPIRGLDGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12691
Length:	389 (300)
Sequences:	6433 (5657)
Seq/√Len:	326.6

ECOLI - LPSRP HEMY NLPI YBEQ PGAA
BACSU - YVCD YPIA RAPE RAPB RAPH RAPI RAPG RAPA RAPD RAPJ RAPF RAPK RAPC YRRB
SULSO - Q97VC4 Q97V36 Q97WM3 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
264_K	267_E	4.683	1.00
195_D	198_R	4.594	1.00
229_E	232_K	4.524	1.00
84_E	87_R	4.353	1.00
156_E	159_K	4.271	1.00
122_L	125_R	4.239	1.00
297_G	300_A	4.058	1.00
50_Q	53_K	3.896	1.00
76_G	92_H	2.899	1.00
187_A	203_L	2.758	1.00
42_G	58_F	2.493	1.00
148_L	164_A	2.475	1.00
256_Q	272_L	2.409	1.00
114_G	130_F	2.308	1.00
221_G	237_L	2.306	1.00
183_Y	202_L	2.246	1.00
110_I	129_M	2.232	1.00
289_A	305_I	2.083	1.00
58_F	74_T	2.056	1.00
285_E	304_Y	2.054	1.00
144_L	163_V	2.030	1.00
72_H	91_I	2.025	1.00
93_Q	113_L	1.993	1.00
130_F	146_Q	1.983	1.00
224_F	232_K	1.978	1.00
186_L	202_L	1.957	1.00
252_L	271_F	1.892	1.00
190_H	198_R	1.890	1.00
269_A	273_Q	1.857	1.00
131_N	147_L	1.855	1.00
75_L	79_F	1.826	1.00
165_E	186_L	1.811	1.00
92_H	112_Q	1.804	1.00
75_L	91_I	1.803	1.00
288_L	292_I	1.794	1.00
200_M	204_K	1.782	1.00
151_Y	159_K	1.776	1.00
59_L	75_L	1.754	1.00
203_L	219_M	1.740	1.00
147_L	163_V	1.714	1.00
113_L	129_M	1.708	1.00
198_R	201_T	1.676	1.00
237_L	254_M	1.665	1.00
204_K	220_M	1.659	1.00
217_S	236_S	1.649	1.00
161_I	186_L	1.627	1.00
164_A	185_E	1.618	1.00
186_L	190_H	1.599	1.00
127_E	147_L	1.591	1.00
117_Y	129_M	1.590	1.00
117_Y	125_R	1.585	1.00
256_Q	275_A	1.567	1.00
79_F	84_E	1.565	1.00
76_G	95_L	1.560	1.00
117_Y	122_L	1.548	1.00
200_M	220_M	1.545	1.00
220_M	236_S	1.541	1.00
200_M	224_F	1.540	1.00
161_I	165_E	1.526	1.00
55_V	79_F	1.516	1.00
273_Q	288_L	1.514	1.00
220_M	224_F	1.512	1.00
224_F	236_S	1.511	1.00
255_L	259_Y	1.483	1.00
79_F	91_I	1.479	1.00
79_F	87_R	1.477	1.00
113_L	117_Y	1.466	1.00
238_Q	255_L	1.458	1.00
60_D	63_K	1.424	1.00
234_V	258_C	1.418	1.00
147_L	151_Y	1.410	1.00
148_L	167_L	1.405	1.00
234_V	238_Q	1.388	1.00
292_I	300_A	1.383	1.00
190_H	195_D	1.381	1.00
259_Y	264_K	1.375	1.00
111_Q	146_Q	1.362	1.00
72_H	94_T	1.362	1.00
159_K	162_D	1.356	1.00
190_H	202_L	1.352	1.00
45_F	50_Q	1.346	1.00
234_V	262_L	1.346	1.00
218_I	254_M	1.341	1.00
302_Q	306_T	1.338	1.00
234_V	255_L	1.327	1.00
144_L	166_R	1.327	1.00
55_V	75_L	1.326	1.00
52_D	82_R	1.324	1.00
200_M	227_K	1.311	1.00
45_F	53_K	1.311	1.00
42_G	61_M	1.302	1.00
124_D	154_T	1.301	1.00
272_L	287_M	1.289	1.00
224_F	229_E	1.281	1.00
41_A	45_F	1.278	1.00
259_Y	267_E	1.272	1.00
158_Q	193_S	1.261	1.00
110_I	133_L	1.261	1.00
127_E	151_Y	1.248	1.00
89_I	113_L	1.247	1.00
125_R	128_D	1.245	1.00
221_G	240_V	1.243	1.00
151_Y	156_E	1.241	1.00
234_V	259_Y	1.225	1.00
145_Q	185_E	1.225	1.00
127_E	131_N	1.202	1.00
184_C	219_M	1.196	1.00
200_M	223_V	1.187	1.00
255_L	271_F	1.169	1.00
94_T	97_E	1.167	1.00
183_Y	205_K	1.164	1.00
89_I	116_D	1.151	1.00
259_Y	271_F	1.147	1.00
231_A	262_L	1.144	1.00
232_K	235_E	1.143	1.00
39_Y	43_V	1.142	1.00
269_A	295_R	1.141	1.00
289_A	308_Q	1.138	1.00
69_V	95_L	1.133	1.00
267_E	270_E	1.129	1.00
46_L	58_F	1.120	1.00
127_E	154_T	1.109	1.00
167_L	182_F	1.095	1.00
73_L	112_Q	1.093	1.00
222_R	254_M	1.092	1.00
187_A	206_G	1.088	1.00
53_K	56_D	1.086	1.00
89_I	120_A	1.086	1.00
241_I	251_T	1.086	1.00
225_M	237_L	1.081	1.00
217_S	239_R	1.078	1.00
222_R	237_L	1.077	1.00
292_I	297_G	1.073	1.00
163_V	167_L	1.062	1.00
188_L	219_M	1.056	1.00
300_A	303_V	1.054	1.00
205_K	208_A	1.051	1.00
239_R	242_S	1.044	1.00
266_A	295_R	1.033	1.00
76_G	88_A	1.029	1.00
288_L	304_Y	1.027	1.00
197_D	227_K	1.026	1.00
274_R	277_E	1.021	1.00
151_Y	163_V	1.020	1.00
240_V	251_T	1.019	1.00
168_V	182_F	1.017	1.00
269_A	291_I	1.015	1.00
256_Q	268_W	1.002	1.00
187_A	202_L	1.000	1.00
80_R	116_D	1.000	1.00
42_G	54_A	0.999	1.00
103_Y	106_R	0.990	1.00
207_A	217_S	0.988	1.00
161_I	193_S	0.983	1.00
86_D	120_A	0.978	1.00
107_L	133_L	0.976	1.00
161_I	190_H	0.975	1.00
96_M	110_I	0.974	1.00
149_Q	185_E	0.972	1.00
89_I	93_Q	0.967	1.00
161_I	189_Q	0.965	1.00
196_L	223_V	0.964	1.00
55_V	59_L	0.964	1.00
223_V	227_K	0.960	1.00
93_Q	97_E	0.955	1.00
289_A	301_A	0.954	1.00
110_I	132_Q	0.952	1.00
80_R	92_H	0.952	1.00
286_L	289_A	0.942	1.00
191_M	203_L	0.942	1.00
206_G	216_V	0.942	1.00
45_F	57_L	0.932	1.00
206_G	209_A	0.929	1.00
207_A	216_V	0.927	1.00
144_L	167_L	0.923	1.00
221_G	233_A	0.918	1.00
114_G	129_M	0.918	1.00
106_R	110_I	0.918	1.00
252_L	274_R	0.918	1.00
38_D	61_M	0.916	1.00
292_I	304_Y	0.915	1.00
291_I	295_R	0.914	1.00
65_D	68_T	0.913	1.00
38_D	57_L	0.911	1.00
258_C	262_L	0.908	1.00
303_V	307_R	0.903	1.00
241_I	252_L	0.903	1.00
269_A	288_L	0.897	1.00
43_V	58_F	0.893	1.00
35_L	61_M	0.891	1.00
213_S	217_S	0.891	1.00
337_S	341_L	0.888	1.00
273_Q	277_E	0.887	1.00
95_L	98_S	0.875	1.00
166_R	169_K	0.874	1.00
132_Q	135_D	0.869	1.00
88_A	92_H	0.867	1.00
55_V	82_R	0.865	1.00
267_E	271_F	0.863	1.00
254_M	257_T	0.862	1.00
137_T	140_R	0.860	1.00
133_L	143_A	0.860	1.00
184_C	216_V	0.859	1.00
225_M	230_Y	0.858	1.00
87_R	90_R	0.858	1.00
55_V	78_L	0.857	1.00
62_L	71_A	0.849	1.00
218_I	222_R	0.847	1.00
46_L	51_Q	0.840	1.00
114_G	133_L	0.840	1.00
62_L	72_H	0.839	1.00
205_K	209_A	0.836	1.00
335_K	339_M	0.831	1.00
57_L	61_M	0.830	1.00
188_L	203_L	0.828	1.00
221_G	236_S	0.826	1.00
253_E	257_T	0.823	1.00
230_Y	258_C	0.814	1.00
78_L	82_R	0.814	1.00
165_E	198_R	0.813	1.00
116_D	120_A	0.809	1.00
129_M	133_L	0.804	1.00
148_L	163_V	0.803	1.00
274_R	278_E	0.801	1.00
152_Q	189_Q	0.801	1.00
275_A	284_A	0.799	1.00
148_L	160_A	0.799	1.00
339_M	342_R	0.794	1.00
213_S	216_V	0.784	1.00
61_M	64_E	0.782	1.00
127_E	150_I	0.779	1.00
133_L	136_E	0.778	1.00
69_V	76_G	0.778	1.00
59_L	63_K	0.778	1.00
260_Q	272_L	0.775	1.00
146_Q	149_Q	0.770	1.00
304_Y	307_R	0.770	1.00
198_R	202_L	0.769	1.00
36_S	40_V	0.768	1.00
145_Q	182_F	0.767	1.00
183_Y	206_G	0.767	1.00
321_L	325_H	0.763	1.00
152_Q	164_A	0.760	1.00
43_V	74_T	0.757	0.99
334_A	341_L	0.756	0.99
46_L	74_T	0.755	0.99
333_R	336_E	0.751	0.99
162_D	165_E	0.748	0.99
93_Q	117_Y	0.747	0.99
337_S	340_V	0.746	0.99
307_R	310_Q	0.743	0.99
164_A	168_V	0.742	0.99
37_R	41_A	0.741	0.99
111_Q	115_R	0.738	0.99
96_M	109_A	0.735	0.99
149_Q	164_A	0.734	0.99
230_Y	234_V	0.725	0.99
134_T	143_A	0.725	0.99
89_I	117_Y	0.723	0.99
68_T	71_A	0.721	0.99
338_L	341_L	0.721	0.99
96_M	113_L	0.718	0.99
51_Q	78_L	0.718	0.99
160_A	189_Q	0.715	0.99
44_N	48_S	0.714	0.99
167_L	170_L	0.713	0.99
80_R	112_Q	0.711	0.99
95_L	109_A	0.709	0.99
273_Q	300_A	0.707	0.99
191_M	196_L	0.705	0.99
214_A	240_V	0.700	0.99
183_Y	186_L	0.699	0.99
162_D	166_R	0.698	0.99
91_I	95_L	0.698	0.99
42_G	57_L	0.697	0.99
189_Q	193_S	0.696	0.99
74_T	77_N	0.695	0.99
111_Q	143_A	0.694	0.99
165_E	190_H	0.694	0.99
34_R	38_D	0.692	0.99
77_N	112_Q	0.691	0.99
187_A	199_A	0.691	0.99
94_T	98_S	0.691	0.99
163_V	166_R	0.687	0.99
72_H	95_L	0.686	0.99
41_A	57_L	0.684	0.99
74_T	112_Q	0.681	0.99
286_L	290_D	0.678	0.99
126_A	150_I	0.677	0.99
86_D	90_R	0.676	0.99
77_N	81_S	0.675	0.99
38_D	60_D	0.672	0.99
61_M	71_A	0.671	0.99
165_E	169_K	0.669	0.99
276_V	285_E	0.668	0.99
260_Q	291_I	0.667	0.99
56_D	60_D	0.667	0.99
287_M	290_D	0.665	0.99
324_Y	328_E	0.665	0.99
134_T	144_L	0.665	0.99
201_T	205_K	0.665	0.99
60_D	64_E	0.665	0.99
271_F	274_R	0.664	0.99
253_E	275_A	0.663	0.99
114_G	147_L	0.661	0.99
71_A	74_T	0.661	0.99
218_I	251_T	0.658	0.99
114_G	126_A	0.656	0.99
319_H	323_D	0.654	0.99
115_R	146_Q	0.654	0.99
203_L	223_V	0.651	0.98
332_G	337_S	0.650	0.98
300_A	304_Y	0.647	0.98
225_M	258_C	0.647	0.98
38_D	64_E	0.647	0.98
166_R	170_L	0.647	0.98
37_R	40_V	0.646	0.98
236_S	240_V	0.644	0.98
222_R	225_M	0.642	0.98
304_Y	308_Q	0.641	0.98
136_E	141_I	0.638	0.98
131_N	159_K	0.637	0.98
128_D	132_Q	0.636	0.98
336_E	340_V	0.635	0.98
204_K	224_F	0.635	0.98
46_L	78_L	0.634	0.98
253_E	284_A	0.631	0.98
57_L	60_D	0.631	0.98
318_F	321_L	0.630	0.98
190_H	193_S	0.630	0.98
203_L	220_M	0.628	0.98
168_V	183_Y	0.628	0.98
196_L	227_K	0.625	0.98
285_E	307_R	0.624	0.98
257_T	260_Q	0.624	0.98
118_M	130_F	0.623	0.98
54_A	58_F	0.621	0.98
31_E	34_R	0.621	0.98
38_D	41_A	0.621	0.98
329_A	334_A	0.618	0.98
73_L	95_L	0.618	0.98
232_K	236_S	0.618	0.98
237_L	241_I	0.618	0.98
143_A	146_Q	0.616	0.98
336_E	339_M	0.614	0.98
269_A	292_I	0.613	0.98
285_E	308_Q	0.612	0.98
265_T	269_A	0.608	0.98
225_M	261_Q	0.608	0.98
265_T	291_I	0.607	0.98
219_M	222_R	0.607	0.98
272_L	276_V	0.607	0.98
184_C	188_L	0.606	0.98
234_V	264_K	0.606	0.98
240_V	243_Q	0.606	0.98
125_R	129_M	0.605	0.98
37_R	44_N	0.599	0.97
73_L	77_N	0.598	0.97
204_K	208_A	0.594	0.97
188_L	191_M	0.593	0.97
184_C	206_G	0.591	0.97
260_Q	265_T	0.588	0.97
236_S	239_R	0.584	0.97
204_K	232_K	0.584	0.97
91_I	98_S	0.583	0.97
306_T	310_Q	0.581	0.97
59_L	87_R	0.581	0.97
168_V	186_L	0.580	0.97
171_G	182_F	0.580	0.97
253_E	256_Q	0.578	0.97
114_G	146_Q	0.577	0.97
275_A	278_E	0.575	0.97
333_R	337_S	0.574	0.97
225_M	233_A	0.574	0.97
89_I	96_M	0.573	0.97
34_R	37_R	0.572	0.97
92_H	113_L	0.571	0.97
74_T	78_L	0.570	0.96
298_S	302_Q	0.569	0.96
260_Q	294_A	0.566	0.96
332_G	335_K	0.565	0.96
238_Q	259_Y	0.565	0.96
137_T	141_I	0.565	0.96
123_Y	127_E	0.564	0.96
259_Y	262_L	0.560	0.96
256_Q	271_F	0.559	0.96
69_V	72_H	0.559	0.96
68_T	72_H	0.559	0.96
257_T	272_L	0.559	0.96
191_M	223_V	0.558	0.96
118_M	153_A	0.557	0.96
43_V	47_L	0.557	0.96
118_M	150_I	0.557	0.96
257_T	287_M	0.557	0.96
322_M	326_L	0.555	0.96
152_Q	157_W	0.555	0.96
180_A	206_G	0.555	0.96
140_R	143_A	0.553	0.96
56_D	59_L	0.552	0.96
338_L	342_R	0.551	0.96
183_Y	187_A	0.551	0.96
91_I	94_T	0.551	0.96
241_I	247_L	0.549	0.96
233_A	237_L	0.549	0.96
318_F	325_H	0.548	0.96
80_R	85_V	0.548	0.96
130_F	147_L	0.547	0.96
90_R	94_T	0.543	0.95
76_G	112_Q	0.541	0.95
238_Q	242_S	0.540	0.95
144_L	170_L	0.539	0.95
334_A	338_L	0.538	0.95
289_A	293_E	0.535	0.95
299_E	303_V	0.535	0.95
225_M	254_M	0.534	0.95
315_M	319_H	0.533	0.95
276_V	284_A	0.532	0.95
93_Q	125_R	0.532	0.95
334_A	337_S	0.531	0.95
335_K	342_R	0.531	0.95
217_S	252_L	0.529	0.95
237_L	258_C	0.528	0.95
39_Y	71_A	0.527	0.95
92_H	116_D	0.526	0.95
131_N	135_D	0.526	0.95
196_L	200_M	0.526	0.95
76_G	91_I	0.526	0.95
207_A	220_M	0.524	0.94
202_L	206_G	0.524	0.94
238_Q	267_E	0.524	0.94
271_F	275_A	0.523	0.94
157_W	196_L	0.523	0.94
45_F	48_S	0.522	0.94
214_A	221_G	0.521	0.94
260_Q	287_M	0.521	0.94
88_A	116_D	0.520	0.94
217_S	224_F	0.520	0.94
329_A	335_K	0.518	0.94
270_E	274_R	0.516	0.94
329_A	333_R	0.515	0.94
247_L	251_T	0.514	0.94
224_F	227_K	0.512	0.94
307_R	311_R	0.511	0.94
285_E	311_R	0.508	0.93
132_Q	136_E	0.507	0.93
39_Y	74_T	0.507	0.93
145_Q	149_Q	0.507	0.93
79_F	82_R	0.502	0.93
191_M	226_A	0.501	0.93
124_D	128_D	0.500	0.93

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
1w3bA	2	0.9126	100	0.293	Contact Map
2xpiA	2	0.8149	100	0.325	Contact Map
4rg9A	2	0.7558	100	0.338	Contact Map
5aioA	1	0.7686	100	0.338	Contact Map
4ui9J	2	0.838	100	0.338	Contact Map
4ui9F	2	0.8149	100	0.341	Contact Map
4ui9C	2	0.8201	100	0.342	Contact Map
2y4tA	1	0.8869	100	0.346	Contact Map
3dssA	1	0.7018	100	0.346	Contact Map
4l9pA	1	0.7455	100	0.353	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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