NIKC - ECOLI - GREMLIN Contacts

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NIKC - Nickel transport system permease protein NikC

UniProt:	P0AFA9	Sequences: MNFFLSSRWSVRLALIIIALLALIALTSQWWLPYDPQAIDLPSRLLSPDAQHWLGTDHLGRDIFSRLMAATRVSLGSVMACLLLVLTLGLVIGGSAGLIGGRVDQATMRVADMFMTFPTSILSFFMVGVLGTGLTNVIIAIALSHWAWYARMVRSLVISLRQREFVLASRLSGAGHVRVFVDHLAGAVIPSLLVLATLDIGHMMLHVAGMSFLGLGVTAPTAEWGVMINDARQYIWTQPLQMFWPGLALFISVMAFNLVGDALRDHLDPHLVTEHAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12077
Length:	277 (253)
Sequences:	28653 (18128)
Seq/√Len:	1139.7

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_V	184_L	2.851	1.00
104_D	154_R	2.692	1.00
160_L	165_F	2.490	1.00
170_R	176_H	2.486	1.00
174_A	178_R	2.478	1.00
178_R	182_D	2.462	1.00
92_I	107_T	2.418	1.00
80_A	138_I	2.389	1.00
160_L	163_R	2.375	1.00
84_L	142_A	2.361	1.00
175_G	178_R	2.322	1.00
73_V	212_F	2.317	1.00
177_V	181_V	2.262	1.00
40_D	43_S	2.175	1.00
226_V	230_D	2.156	1.00
164_E	167_L	2.151	1.00
166_V	179_V	2.081	1.00
166_V	184_L	2.050	1.00
50_A	53_W	2.027	1.00
94_G	157_V	2.014	1.00
66_R	227_M	1.995	1.00
197_T	260_G	1.994	1.00
95_S	99_I	1.951	1.00
99_I	176_H	1.902	1.00
99_I	103_V	1.897	1.00
62_D	65_S	1.891	1.00
87_T	91_V	1.877	1.00
149_Y	199_D	1.854	1.00
35_D	38_A	1.832	1.00
160_L	188_V	1.776	1.00
57_D	61_R	1.772	1.00
19_A	23_L	1.764	1.00
98_L	176_H	1.764	1.00
165_F	187_A	1.763	1.00
97_G	157_V	1.754	1.00
102_R	106_A	1.734	1.00
25_A	71_T	1.734	1.00
59_L	66_R	1.672	1.00
95_S	103_V	1.660	1.00
88_L	91_V	1.655	1.00
64_F	68_M	1.650	1.00
88_L	146_W	1.648	1.00
161_R	184_L	1.644	1.00
54_L	244_W	1.643	1.00
85_V	145_H	1.603	1.00
76_G	80_A	1.591	1.00
52_H	62_D	1.586	1.00
69_A	72_R	1.579	1.00
156_L	159_S	1.564	1.00
63_I	244_W	1.560	1.00
103_V	107_T	1.555	1.00
138_I	142_A	1.553	1.00
111_A	150_A	1.538	1.00
231_A	241_Q	1.519	1.00
86_L	196_A	1.518	1.00
98_L	180_F	1.515	1.00
58_H	230_D	1.506	1.00
11_V	262_A	1.500	1.00
107_T	150_A	1.490	1.00
61_R	65_S	1.483	1.00
159_S	163_R	1.478	1.00
93_G	97_G	1.468	1.00
89_G	149_Y	1.451	1.00
228_I	245_P	1.445	1.00
27_T	30_W	1.424	1.00
82_L	196_A	1.400	1.00
14_A	255_A	1.398	1.00
121_I	125_F	1.373	1.00
109_R	112_D	1.363	1.00
154_R	158_I	1.359	1.00
93_G	153_V	1.359	1.00
102_R	105_Q	1.354	1.00
168_A	172_S	1.349	1.00
97_G	161_R	1.322	1.00
73_V	76_G	1.322	1.00
92_I	150_A	1.314	1.00
89_G	153_V	1.311	1.00
194_V	264_R	1.310	1.00
135_T	139_I	1.302	1.00
54_L	64_F	1.290	1.00
43_S	46_L	1.287	1.00
160_L	166_V	1.282	1.00
201_G	253_V	1.281	1.00
67_L	248_A	1.272	1.00
126_M	140_A	1.271	1.00
263_L	266_H	1.270	1.00
12_R	16_I	1.268	1.00
96_A	107_T	1.265	1.00
94_G	180_F	1.263	1.00
21_L	250_F	1.263	1.00
152_M	195_L	1.260	1.00
239_P	243_F	1.254	1.00
142_A	146_W	1.250	1.00
23_L	27_T	1.236	1.00
193_L	267_L	1.231	1.00
160_L	184_L	1.226	1.00
264_R	268_D	1.225	1.00
61_R	66_R	1.208	1.00
169_S	183_H	1.204	1.00
49_D	54_L	1.197	1.00
9_W	12_R	1.196	1.00
169_S	174_A	1.175	1.00
77_S	207_V	1.164	1.00
169_S	179_V	1.157	1.00
157_V	188_V	1.143	1.00
94_G	185_A	1.134	1.00
114_F	147_A	1.128	1.00
61_R	69_A	1.127	1.00
153_V	192_L	1.121	1.00
167_L	170_R	1.112	1.00
262_A	266_H	1.107	1.00
18_I	251_I	1.105	1.00
105_Q	109_R	1.099	1.00
153_V	157_V	1.097	1.00
100_G	161_R	1.091	1.00
90_L	153_V	1.089	1.00
178_R	181_V	1.083	1.00
133_G	136_N	1.082	1.00
245_P	249_L	1.070	1.00
54_L	67_L	1.064	1.00
156_L	160_L	1.060	1.00
91_V	94_G	1.059	1.00
227_M	241_Q	1.050	1.00
140_A	144_S	1.049	1.00
231_A	242_M	1.044	1.00
123_S	140_A	1.040	1.00
72_R	76_G	1.038	1.00
110_V	114_F	1.038	1.00
146_W	150_A	1.038	1.00
56_T	62_D	1.037	1.00
117_F	122_L	1.037	1.00
104_D	108_M	1.034	1.00
135_T	138_I	1.031	1.00
172_S	183_H	1.027	1.00
28_S	69_A	1.023	1.00
13_L	16_I	1.023	1.00
81_C	142_A	1.021	1.00
108_M	150_A	1.018	1.00
63_I	241_Q	1.016	1.00
14_A	262_A	1.010	1.00
100_G	162_Q	1.005	1.00
16_I	20_L	1.001	1.00
32_L	65_S	0.998	1.00
170_R	179_V	0.991	1.00
63_I	227_M	0.981	1.00
14_A	254_M	0.975	1.00
21_L	252_S	0.975	1.00
169_S	172_S	0.969	1.00
240_L	244_W	0.968	1.00
81_C	85_V	0.964	1.00
66_R	241_Q	0.962	1.00
104_D	158_I	0.961	1.00
153_V	188_V	0.961	1.00
18_I	255_A	0.959	1.00
76_G	134_L	0.958	1.00
20_L	24_I	0.957	1.00
16_I	19_A	0.951	1.00
200_I	256_F	0.950	1.00
17_I	255_A	0.947	1.00
65_S	69_A	0.943	1.00
67_L	244_W	0.940	1.00
76_G	79_M	0.936	1.00
130_L	136_N	0.932	1.00
49_D	53_W	0.930	1.00
70_A	227_M	0.930	1.00
81_C	141_I	0.922	1.00
34_Y	51_Q	0.921	1.00
49_D	52_H	0.921	1.00
52_H	56_T	0.918	1.00
119_T	206_H	0.917	1.00
14_A	258_L	0.917	1.00
174_A	179_V	0.915	1.00
176_H	179_V	0.910	1.00
244_W	247_L	0.907	1.00
106_A	110_V	0.906	1.00
15_L	19_A	0.906	1.00
190_P	264_R	0.904	1.00
105_Q	108_M	0.904	1.00
103_V	106_A	0.897	1.00
46_L	49_D	0.892	1.00
93_G	157_V	0.891	1.00
58_H	234_Y	0.890	1.00
255_A	259_V	0.874	1.00
56_T	60_G	0.871	1.00
15_L	259_V	0.863	1.00
11_V	258_L	0.858	1.00
42_P	46_L	0.857	1.00
141_I	206_H	0.856	1.00
87_T	90_L	0.854	1.00
24_I	68_M	0.852	1.00
66_R	69_A	0.850	1.00
111_A	147_A	0.850	1.00
195_L	199_D	0.849	1.00
86_L	90_L	0.849	1.00
68_M	72_R	0.848	1.00
90_L	192_L	0.847	1.00
17_I	251_I	0.847	1.00
188_V	191_S	0.841	1.00
181_V	184_L	0.838	1.00
86_L	91_V	0.837	1.00
34_Y	65_S	0.835	1.00
134_L	138_I	0.834	1.00
256_F	260_G	0.828	1.00
193_L	260_G	0.823	1.00
119_T	123_S	0.818	1.00
34_Y	52_H	0.816	1.00
91_V	95_S	0.814	1.00
157_V	161_R	0.807	1.00
30_W	239_P	0.801	1.00
227_M	245_P	0.799	1.00
163_R	167_L	0.793	1.00
86_L	149_Y	0.792	1.00
71_T	252_S	0.789	1.00
155_S	158_I	0.788	1.00
65_S	68_M	0.786	1.00
101_G	104_D	0.784	1.00
81_C	203_M	0.782	1.00
176_H	180_F	0.782	1.00
79_M	83_L	0.782	1.00
126_M	136_N	0.782	1.00
139_I	142_A	0.781	1.00
43_S	52_H	0.781	1.00
160_L	187_A	0.777	1.00
84_L	138_I	0.776	1.00
92_I	146_W	0.775	1.00
96_A	104_D	0.775	1.00
174_A	183_H	0.775	1.00
97_G	158_I	0.774	1.00
243_F	247_L	0.772	1.00
33_P	65_S	0.763	1.00
115_M	147_A	0.761	1.00
136_N	139_I	0.761	1.00
44_R	48_P	0.760	1.00
11_V	15_L	0.751	1.00
264_R	271_L	0.749	1.00
229_N	232_R	0.749	1.00
74_S	78_V	0.746	1.00
27_T	31_W	0.745	1.00
179_V	184_L	0.745	1.00
265_D	271_L	0.739	1.00
167_L	171_L	0.738	1.00
80_A	212_F	0.731	1.00
68_M	71_T	0.727	1.00
101_G	105_Q	0.722	1.00
249_L	253_V	0.722	1.00
244_W	248_A	0.721	1.00
22_A	247_L	0.719	1.00
80_A	83_L	0.719	1.00
156_L	191_S	0.718	1.00
153_V	156_L	0.713	1.00
10_S	14_A	0.708	1.00
230_D	233_Q	0.700	1.00
88_L	142_A	0.700	1.00
53_W	64_F	0.699	1.00
251_I	255_A	0.699	1.00
24_I	71_T	0.698	1.00
201_G	256_F	0.697	1.00
26_L	30_W	0.694	1.00
131_G	135_T	0.691	1.00
49_D	247_L	0.680	1.00
21_L	251_I	0.680	1.00
156_L	188_V	0.676	1.00
243_F	246_G	0.674	1.00
89_G	93_G	0.673	1.00
145_H	148_W	0.673	1.00
259_V	263_L	0.670	1.00
57_D	238_Q	0.670	1.00
53_W	62_D	0.668	1.00
14_A	17_I	0.667	1.00
144_S	147_A	0.664	1.00
197_T	256_F	0.663	1.00
85_V	142_A	0.663	1.00
45_L	48_P	0.662	1.00
13_L	17_I	0.659	1.00
100_G	104_D	0.659	1.00
177_V	180_F	0.657	1.00
28_S	31_W	0.654	1.00
205_L	208_A	0.652	1.00
34_Y	237_T	0.651	1.00
48_P	240_L	0.649	1.00
205_L	209_G	0.647	1.00
137_V	207_V	0.645	1.00
207_V	211_S	0.642	1.00
253_V	257_N	0.639	1.00
88_L	92_I	0.638	1.00
98_L	161_R	0.637	1.00
9_W	13_L	0.635	1.00
33_P	64_F	0.635	1.00
119_T	122_L	0.635	1.00
67_L	245_P	0.632	1.00
96_A	108_M	0.628	1.00
158_I	161_R	0.628	1.00
18_I	256_F	0.625	1.00
42_P	45_L	0.625	1.00
100_G	158_I	0.619	1.00
106_A	109_R	0.618	1.00
208_A	226_V	0.618	1.00
82_L	199_D	0.615	1.00
24_I	28_S	0.613	1.00
29_Q	72_R	0.613	1.00
12_R	15_L	0.608	1.00
82_L	200_I	0.608	1.00
107_T	111_A	0.606	1.00
242_M	246_G	0.604	1.00
111_A	146_W	0.603	1.00
108_M	111_A	0.602	1.00
206_H	209_G	0.601	1.00
99_I	180_F	0.596	1.00
80_A	135_T	0.595	1.00
174_A	177_V	0.590	1.00
78_V	203_M	0.589	1.00
97_G	104_D	0.588	1.00
125_F	129_V	0.587	1.00
98_L	181_V	0.587	1.00
148_W	199_D	0.587	1.00
45_L	238_Q	0.587	1.00
75_L	79_M	0.586	1.00
37_Q	41_L	0.586	1.00
17_I	21_L	0.585	1.00
41_L	44_R	0.585	1.00
109_R	113_M	0.583	1.00
149_Y	153_V	0.582	1.00
114_F	146_W	0.581	1.00
131_G	136_N	0.580	1.00
40_D	52_H	0.580	1.00
143_L	146_W	0.579	1.00
47_S	240_L	0.578	1.00
229_N	233_Q	0.578	1.00
227_M	230_D	0.577	1.00
265_D	272_V	0.575	1.00
149_Y	195_L	0.575	1.00
71_T	75_L	0.573	1.00
119_T	143_L	0.567	1.00
203_M	206_H	0.567	1.00
122_L	144_S	0.565	1.00
204_M	208_A	0.561	1.00
72_R	75_L	0.559	1.00
25_A	246_G	0.559	1.00
83_L	87_T	0.558	1.00
194_V	197_T	0.556	1.00
32_L	69_A	0.556	1.00
230_D	234_Y	0.549	1.00
166_V	170_R	0.548	1.00
136_N	140_A	0.545	1.00
208_A	229_N	0.543	1.00
86_L	192_L	0.543	1.00
208_A	230_D	0.542	1.00
14_A	18_I	0.541	1.00
77_S	137_V	0.538	1.00
112_D	115_M	0.537	1.00
139_I	143_L	0.537	1.00
89_G	150_A	0.537	1.00
82_L	86_L	0.536	1.00
29_Q	69_A	0.535	1.00
258_L	262_A	0.533	1.00
66_R	70_A	0.532	1.00
40_D	44_R	0.531	1.00
227_M	231_A	0.530	1.00
18_I	259_V	0.528	1.00
228_I	249_L	0.528	1.00
108_M	112_D	0.527	1.00
145_H	199_D	0.526	1.00
240_L	243_F	0.525	1.00
96_A	154_R	0.524	1.00
10_S	258_L	0.518	1.00
45_L	241_Q	0.516	1.00
46_L	56_T	0.516	1.00
175_G	179_V	0.515	1.00
92_I	95_S	0.515	1.00
21_L	25_A	0.515	1.00
147_A	150_A	0.514	1.00
199_D	203_M	0.510	1.00
181_V	186_G	0.507	1.00
78_V	200_I	0.507	1.00
148_W	195_L	0.506	1.00
152_M	156_L	0.506	1.00
44_R	47_S	0.505	1.00
189_I	193_L	0.504	1.00
39_I	59_L	0.501	1.00
142_A	145_H	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
4tquM	1	0.9061	99.9	0.577	Contact Map
3tuiA	2	0.7329	99.9	0.613	Contact Map
3d31C	2	0.8339	99.9	0.63	Contact Map
3rlfF	1	0.9061	99.9	0.633	Contact Map
3rlfG	1	0.935	99.9	0.638	Contact Map
4tquN	1	0.9278	99.8	0.642	Contact Map
2onkC	2	0.852	99.8	0.642	Contact Map
4ymuD	2	0.7545	99.8	0.648	Contact Map
3j9pD	4	0.7798	62	0.933	Contact Map
2k1eA	3	0.361	14.6	0.952	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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