NIKB - ECOLI - GREMLIN Contacts

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NIKB - Nickel transport system permease protein NikB

UniProt:	P33591	Sequences: MLRYVLRRFLLLIPMVLAASVIIFLMLRLGTGDPALDYLRLSNLPPTPEMLASTRTMLGLDQPLYVQYGTWLWKALHLDFGISFASQRPVLDDMLNFLPATLELAGAALVLILLTSVPLGIWAARHRDRLPDFAVRFIAFLGVSMPNFWLAFLLVMAFSVYLQWLPAMGYGGWQHIILPAVSIAFMSLAINARLLRASMLDVAGQRHVTWARLRGLNDKQTERRHILRNASLPMITAVGMHIGELIGGTMIIENIFAWPGVGRYAVSAIFNRDYPVIQCFTLMMVVVFVVCNLIVDLLNAALDPRIRRHEGAHA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12076
Length:	314 (298)
Sequences:	20059 (13016)
Seq/√Len:	754.0

ECOLI - NIKB YEJB DDPB DPPB GSIC OPPB SAPB YEJE DPPC SAPC NIKC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMW3 Q9HMI2 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VF8 Q97YQ0 Q97UH1 Q97VK6 Q97UG4 Q97YP1 Q97VK7 Q97UG3 Q97YP2 Q97YP9 Q97UH2 Q97VF6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_Q	66_V	3.339	1.00
62_Q	70_T	3.233	1.00
28_R	67_Q	3.179	1.00
73_W	77_H	2.839	1.00
69_G	73_W	2.782	1.00
199_M	226_I	2.748	1.00
56_T	61_D	2.668	1.00
48_P	52_A	2.664	1.00
20_S	68_Y	2.594	1.00
107_A	180_A	2.467	1.00
212_R	218_D	2.450	1.00
220_Q	224_R	2.413	1.00
33_D	55_R	2.390	1.00
100_A	258_W	2.381	1.00
263_R	267_S	2.354	1.00
208_V	226_I	2.272	1.00
202_V	207_H	2.249	1.00
119_L	135_V	2.234	1.00
21_V	68_Y	2.168	1.00
202_V	205_Q	2.128	1.00
93_D	264_Y	2.117	1.00
65_Y	69_G	2.067	1.00
239_G	295_V	2.065	1.00
217_N	220_Q	2.065	1.00
219_K	223_R	2.046	1.00
89_P	92_D	2.039	1.00
50_M	53_S	1.979	1.00
19_A	285_V	1.959	1.00
132_D	196_R	1.949	1.00
51_L	55_R	1.933	1.00
203_A	226_I	1.918	1.00
86_S	93_D	1.909	1.00
111_L	184_A	1.896	1.00
114_L	118_P	1.889	1.00
47_T	50_M	1.862	1.00
216_L	220_Q	1.858	1.00
165_L	174_Q	1.843	1.00
53_S	57_M	1.803	1.00
126_H	129_R	1.801	1.00
208_V	221_T	1.749	1.00
88_R	92_D	1.745	1.00
66_V	70_T	1.739	1.00
159_S	167_A	1.736	1.00
165_L	177_I	1.709	1.00
122_W	126_H	1.707	1.00
90_V	279_C	1.702	1.00
91_L	95_L	1.697	1.00
52_A	55_R	1.684	1.00
130_L	134_A	1.680	1.00
235_I	302_L	1.671	1.00
52_A	56_T	1.661	1.00
74_K	79_D	1.657	1.00
124_A	199_M	1.651	1.00
121_I	199_M	1.595	1.00
126_H	131_P	1.587	1.00
170_Y	258_W	1.587	1.00
210_W	214_R	1.581	1.00
125_R	222_E	1.572	1.00
206_R	209_T	1.566	1.00
122_W	131_P	1.562	1.00
156_M	161_Y	1.561	1.00
180_A	184_A	1.551	1.00
115_T	118_P	1.543	1.00
70_T	73_W	1.535	1.00
131_P	135_V	1.530	1.00
202_V	230_A	1.523	1.00
298_L	301_A	1.514	1.00
265_A	280_F	1.507	1.00
236_T	299_N	1.505	1.00
112_I	187_S	1.501	1.00
12_L	289_V	1.459	1.00
115_T	188_L	1.433	1.00
6_L	10_L	1.430	1.00
149_W	153_L	1.427	1.00
70_T	74_K	1.426	1.00
88_R	96_N	1.425	1.00
202_V	208_V	1.409	1.00
207_H	229_N	1.399	1.00
17_L	68_Y	1.394	1.00
268_A	276_V	1.391	1.00
16_V	286_V	1.388	1.00
103_E	170_Y	1.387	1.00
157_A	161_Y	1.383	1.00
75_A	80_F	1.377	1.00
10_L	14_P	1.375	1.00
202_V	226_I	1.360	1.00
154_L	182_S	1.358	1.00
100_A	170_Y	1.357	1.00
54_T	57_M	1.352	1.00
80_F	279_C	1.351	1.00
17_L	21_V	1.337	1.00
120_G	124_A	1.336	1.00
103_E	107_A	1.322	1.00
128_D	132_D	1.321	1.00
96_N	99_P	1.315	1.00
88_R	93_D	1.301	1.00
113_L	238_V	1.300	1.00
54_T	58_L	1.293	1.00
125_R	218_D	1.290	1.00
35_A	51_L	1.284	1.00
116_S	195_L	1.283	1.00
214_R	225_H	1.281	1.00
116_S	191_N	1.273	1.00
93_D	276_V	1.271	1.00
191_N	241_H	1.266	1.00
33_D	36_L	1.263	1.00
59_G	62_Q	1.251	1.00
109_L	238_V	1.247	1.00
194_L	237_A	1.247	1.00
66_V	69_G	1.243	1.00
264_Y	276_V	1.243	1.00
62_Q	65_Y	1.240	1.00
80_F	91_L	1.237	1.00
184_A	188_L	1.236	1.00
82_I	89_P	1.235	1.00
142_G	189_A	1.224	1.00
100_A	103_E	1.215	1.00
196_R	200_L	1.202	1.00
63_P	66_V	1.201	1.00
124_A	203_A	1.196	1.00
126_H	218_D	1.196	1.00
20_S	71_W	1.194	1.00
76_L	79_D	1.183	1.00
145_M	150_L	1.181	1.00
195_L	234_M	1.171	1.00
120_G	195_L	1.170	1.00
135_V	192_A	1.161	1.00
157_A	162_L	1.154	1.00
297_L	301_A	1.144	1.00
280_F	284_M	1.138	1.00
36_L	51_L	1.134	1.00
119_L	192_A	1.131	1.00
232_L	299_N	1.130	1.00
103_E	176_I	1.128	1.00
123_A	135_V	1.122	1.00
59_G	70_T	1.107	1.00
53_S	56_T	1.100	1.00
130_L	133_F	1.099	1.00
266_V	270_F	1.083	1.00
172_G	175_H	1.082	1.00
243_G	288_F	1.076	1.00
92_D	96_N	1.071	1.00
74_K	77_H	1.070	1.00
173_W	177_I	1.066	1.00
21_V	25_L	1.063	1.00
171_G	175_H	1.060	1.00
182_S	186_M	1.060	1.00
139_A	192_A	1.048	1.00
291_C	295_V	1.044	1.00
16_V	289_V	1.031	1.00
93_D	96_N	1.030	1.00
9_F	293_L	1.024	1.00
95_L	99_P	1.023	1.00
158_F	162_L	1.022	1.00
5_V	297_L	1.020	1.00
18_A	22_I	1.014	1.00
124_A	200_L	1.010	1.00
153_L	157_A	1.007	1.00
17_L	72_L	0.985	1.00
177_I	181_V	0.984	1.00
28_R	64_L	0.982	1.00
108_A	184_A	0.981	1.00
195_L	199_M	0.980	1.00
154_L	178_L	0.979	1.00
165_L	178_L	0.977	1.00
83_S	273_D	0.974	1.00
151_A	182_S	0.971	1.00
83_S	88_R	0.963	1.00
92_D	95_L	0.962	1.00
118_P	121_I	0.956	1.00
218_D	221_T	0.956	1.00
199_M	230_A	0.955	1.00
211_A	216_L	0.954	1.00
12_L	293_L	0.951	1.00
132_D	200_L	0.949	1.00
121_I	222_E	0.948	1.00
39_L	54_T	0.945	1.00
14_P	17_L	0.939	1.00
166_P	169_G	0.936	1.00
242_I	291_C	0.934	1.00
56_T	62_Q	0.934	1.00
105_A	245_L	0.933	1.00
147_N	252_I	0.927	1.00
128_D	133_F	0.926	1.00
35_A	39_L	0.922	1.00
25_L	28_R	0.920	1.00
82_I	87_Q	0.919	1.00
211_A	221_T	0.909	1.00
136_R	192_A	0.907	1.00
216_L	221_T	0.905	1.00
9_F	13_I	0.904	1.00
97_F	264_Y	0.901	1.00
108_A	112_I	0.899	1.00
69_G	72_L	0.895	1.00
267_S	271_N	0.893	1.00
300_A	306_I	0.892	1.00
220_Q	223_R	0.892	1.00
138_I	142_G	0.890	1.00
176_I	180_A	0.889	1.00
49_E	53_S	0.889	1.00
117_V	195_L	0.885	1.00
212_R	221_T	0.884	1.00
294_I	298_L	0.883	1.00
235_I	295_V	0.880	1.00
290_V	294_I	0.879	1.00
274_Y	278_Q	0.875	1.00
116_S	120_G	0.875	1.00
25_L	64_L	0.872	1.00
75_A	282_L	0.870	1.00
111_L	180_A	0.869	1.00
103_E	106_G	0.868	1.00
299_N	306_I	0.867	1.00
73_W	76_L	0.865	1.00
48_P	51_L	0.862	1.00
181_V	184_A	0.860	1.00
21_V	64_L	0.855	1.00
158_F	165_L	0.851	1.00
106_G	110_V	0.850	1.00
188_L	192_A	0.844	1.00
20_S	282_L	0.844	1.00
221_T	226_I	0.844	1.00
267_S	270_F	0.837	1.00
230_A	233_P	0.833	1.00
133_F	136_R	0.833	1.00
28_R	274_Y	0.830	1.00
108_A	183_I	0.827	1.00
32_G	272_R	0.825	1.00
223_R	226_I	0.824	1.00
118_P	122_W	0.817	1.00
120_G	199_M	0.817	1.00
243_G	291_C	0.814	1.00
201_D	205_Q	0.812	1.00
134_A	138_I	0.809	1.00
211_A	225_H	0.809	1.00
72_L	75_A	0.806	1.00
264_Y	268_A	0.805	1.00
94_M	279_C	0.804	1.00
49_E	52_A	0.793	1.00
150_L	185_F	0.790	1.00
113_L	118_P	0.788	1.00
297_L	300_A	0.788	1.00
71_W	75_A	0.786	1.00
101_T	105_A	0.778	1.00
39_L	46_P	0.775	1.00
299_N	303_D	0.775	1.00
46_P	51_L	0.775	1.00
151_A	255_I	0.773	1.00
198_S	202_V	0.769	1.00
177_I	180_A	0.768	1.00
109_L	242_I	0.766	1.00
254_N	263_R	0.764	1.00
68_Y	72_L	0.763	1.00
107_A	258_W	0.762	1.00
286_V	290_V	0.762	1.00
125_R	223_R	0.762	1.00
119_L	188_L	0.759	1.00
195_L	230_A	0.754	1.00
23_I	281_T	0.753	1.00
218_D	222_E	0.753	1.00
84_F	275_P	0.752	1.00
115_T	119_L	0.747	1.00
143_V	189_A	0.747	1.00
198_S	230_A	0.746	1.00
72_L	76_L	0.746	1.00
121_I	227_L	0.745	1.00
117_V	234_M	0.743	1.00
94_M	280_F	0.742	1.00
95_L	98_L	0.737	1.00
198_S	201_D	0.736	1.00
187_S	190_I	0.735	1.00
35_A	55_R	0.735	1.00
104_L	180_A	0.734	1.00
249_T	252_I	0.733	1.00
131_P	134_A	0.729	1.00
90_V	276_V	0.729	1.00
147_N	185_F	0.729	1.00
116_S	192_A	0.727	1.00
90_V	264_Y	0.725	1.00
106_G	242_I	0.724	1.00
155_V	167_A	0.721	1.00
161_Y	164_W	0.717	1.00
254_N	266_V	0.716	1.00
35_A	54_T	0.716	1.00
300_A	307_R	0.710	1.00
264_Y	280_F	0.708	1.00
182_S	252_I	0.707	1.00
73_W	78_L	0.703	1.00
284_M	288_F	0.699	1.00
99_P	102_L	0.699	1.00
279_C	283_M	0.699	1.00
158_F	178_L	0.699	1.00
112_I	184_A	0.698	1.00
99_P	103_E	0.694	1.00
15_M	289_V	0.689	1.00
265_A	268_A	0.689	1.00
38_Y	54_T	0.686	1.00
158_F	164_W	0.686	1.00
142_G	185_F	0.684	1.00
278_Q	281_T	0.681	1.00
156_M	160_V	0.678	1.00
211_A	214_R	0.677	1.00
102_L	106_G	0.677	1.00
139_A	189_A	0.665	1.00
173_W	176_I	0.662	1.00
50_M	54_T	0.661	1.00
27_L	30_G	0.660	1.00
268_A	277_I	0.659	1.00
123_A	132_D	0.657	1.00
259_P	263_R	0.655	1.00
134_A	137_F	0.655	1.00
36_L	40_R	0.651	1.00
288_F	292_N	0.649	1.00
115_T	184_A	0.649	1.00
137_F	140_F	0.648	1.00
195_L	198_S	0.648	1.00
25_L	29_L	0.646	1.00
135_V	139_A	0.646	1.00
170_Y	176_I	0.645	1.00
21_V	65_Y	0.642	1.00
107_A	173_W	0.640	1.00
132_D	136_R	0.639	1.00
168_M	257_A	0.638	1.00
55_R	61_D	0.635	1.00
184_A	187_S	0.630	1.00
14_P	18_A	0.630	1.00
235_I	298_L	0.629	1.00
147_N	151_A	0.624	1.00
46_P	50_M	0.623	1.00
93_D	97_F	0.617	1.00
133_F	137_F	0.616	1.00
10_L	13_I	0.615	1.00
189_A	192_A	0.612	1.00
98_L	102_L	0.609	1.00
104_L	253_E	0.609	1.00
265_A	284_M	0.607	1.00
209_T	212_R	0.606	1.00
278_Q	282_L	0.603	1.00
190_I	237_A	0.599	1.00
254_N	267_S	0.599	1.00
126_H	132_D	0.597	1.00
147_N	150_L	0.596	1.00
101_T	249_T	0.594	1.00
55_R	60_L	0.593	1.00
8_R	296_D	0.592	1.00
97_F	263_R	0.591	1.00
137_F	141_L	0.590	1.00
195_L	227_L	0.589	1.00
231_S	234_M	0.589	1.00
113_L	191_N	0.588	1.00
216_L	225_H	0.587	1.00
13_I	17_L	0.586	1.00
110_V	114_L	0.586	1.00
266_V	269_I	0.584	1.00
239_G	291_C	0.579	1.00
191_N	195_L	0.579	1.00
205_Q	209_T	0.576	1.00
295_V	299_N	0.576	1.00
57_M	87_Q	0.575	1.00
32_G	35_A	0.575	1.00
78_L	82_I	0.575	1.00
190_I	241_H	0.575	1.00
237_A	241_H	0.574	1.00
198_S	233_P	0.570	1.00
165_L	169_G	0.570	1.00
83_S	86_S	0.570	1.00
34_P	37_D	0.569	1.00
108_A	249_T	0.569	1.00
178_L	182_S	0.569	1.00
145_M	149_W	0.569	1.00
107_A	177_I	0.568	1.00
147_N	186_M	0.566	1.00
114_L	117_V	0.566	1.00
191_N	237_A	0.566	1.00
107_A	111_L	0.565	1.00
64_L	67_Q	0.564	1.00
149_W	152_F	0.564	1.00
277_I	281_T	0.564	1.00
232_L	306_I	0.562	1.00
129_R	133_F	0.561	1.00
27_L	277_I	0.561	1.00
219_K	222_E	0.560	1.00
47_T	51_L	0.557	1.00
154_L	181_V	0.557	1.00
35_A	58_L	0.557	1.00
24_F	28_R	0.555	1.00
175_H	178_L	0.555	1.00
250_M	254_N	0.555	1.00
208_V	212_R	0.555	1.00
250_M	266_V	0.554	1.00
223_R	227_L	0.553	1.00
7_R	11_L	0.551	1.00
7_R	10_L	0.551	1.00
223_R	228_R	0.547	1.00
241_H	244_E	0.547	1.00
12_L	15_M	0.546	1.00
125_R	203_A	0.543	1.00
293_L	297_L	0.543	1.00
174_Q	177_I	0.543	1.00
194_L	198_S	0.542	1.00
52_A	61_D	0.542	1.00
105_A	242_I	0.541	1.00
123_A	136_R	0.541	1.00
129_R	134_A	0.540	1.00
209_T	213_L	0.539	1.00
217_N	221_T	0.538	1.00
191_N	234_M	0.538	1.00
113_L	117_V	0.538	1.00
105_A	249_T	0.538	1.00
80_F	94_M	0.538	1.00
75_A	78_L	0.537	1.00
28_R	278_Q	0.536	1.00
105_A	109_L	0.535	1.00
107_A	110_V	0.535	1.00
11_L	15_M	0.533	1.00
35_A	38_Y	0.531	1.00
186_M	189_A	0.529	1.00
199_M	227_L	0.529	1.00
181_V	185_F	0.526	1.00
222_E	226_I	0.524	1.00
166_P	174_Q	0.522	1.00
231_S	235_I	0.521	1.00
187_S	241_H	0.521	1.00
190_I	194_L	0.520	1.00
27_L	31_T	0.520	1.00
287_V	291_C	0.518	1.00
124_A	132_D	0.517	1.00
121_I	223_R	0.517	1.00
168_M	171_G	0.517	1.00
111_L	181_V	0.514	1.00
151_A	155_V	0.513	1.00
107_A	176_I	0.513	1.00
103_E	258_W	0.513	1.00
178_L	181_V	0.513	1.00
19_A	23_I	0.512	1.00
11_L	14_P	0.512	1.00
275_P	278_Q	0.511	1.00
207_H	211_A	0.511	1.00
166_P	175_H	0.510	1.00
276_V	280_F	0.509	1.00
20_S	72_L	0.509	1.00
12_L	16_V	0.507	1.00
149_W	182_S	0.506	1.00
169_G	175_H	0.506	1.00
101_T	253_E	0.503	1.00
173_W	180_A	0.502	1.00
216_L	219_K	0.502	1.00
159_S	178_L	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
3tuiA	2	0.6656	99.9	0.65	Contact Map
4tquM	1	0.8312	99.9	0.665	Contact Map
3rlfF	1	0.8376	99.9	0.674	Contact Map
4ymuD	2	0.6688	99.8	0.69	Contact Map
2onkC	2	0.7739	99.8	0.694	Contact Map
3d31C	2	0.7771	99.8	0.696	Contact Map
4tquN	1	0.8217	99.8	0.71	Contact Map
3rlfG	1	0.8408	99.7	0.72	Contact Map
2yevC	1	0.1083	14.3	0.958	Contact Map
4ltoA	3	0.3344	7	0.964	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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