NicO - PFAM28P - GREMLIN Contacts

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NicO - High-affinity nickel-transport protein

PFAM:	PF03824	Sequences: AWGLGLLAYTLGLRHAFDPDHIKAITRKLLVAGRRPLRVGFFFSLGHSTVVTLLAVALALGALALLGLSALHMVGGVIGTEVASFLLIIAIGNLLVLRGIRRVFRRMRRGGRYDEAELEHLLAHRGLHARLFGPLFRLVDHSWHMYPVGLLFGLGFDTATEVHLLALAAGAAAAGLPFWAILLLPLLFAAGMSLCDTADGVLMLAAYGWAFAKGRKLYYNMTITGLSVTVALLIGGIELLGLLADRLGLSGGFWGALAALDLGLLGYVIVGLFVLTWLVALL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	282 (278)
Sequences:	7824 (5115)
Seq/√Len:	306.8
META:	0.787

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_D	144_H	4.342	1.00
87_L	236_G	3.941	1.00
266_G	269_I	3.541	1.00
122_L	125_R	3.330	1.00
141_H	144_H	2.885	1.00
49_T	146_Y	2.773	1.00
262_L	269_I	2.753	1.00
101_R	221_M	2.676	1.00
171_A	174_A	2.676	1.00
262_L	266_G	2.583	1.00
28_K	32_A	2.512	1.00
258_A	261_D	2.362	1.00
47_H	51_V	2.293	1.00
86_L	90_A	2.269	1.00
81_E	84_S	2.208	1.00
229_T	233_L	2.207	1.00
139_V	148_V	2.195	1.00
38_R	142_S	2.186	1.00
84_S	88_I	2.183	1.00
114_D	117_E	2.096	1.00
74_V	78_I	2.043	1.00
17_F	195_C	2.032	1.00
262_L	265_L	2.021	1.00
267_Y	271_G	2.000	1.00
251_G	255_G	1.991	1.00
52_T	222_T	1.969	1.00
13_L	195_C	1.932	1.00
263_G	266_G	1.923	1.00
55_A	59_A	1.899	1.00
53_L	150_L	1.880	1.00
239_L	242_L	1.855	1.00
166_A	169_A	1.794	1.00
198_A	201_V	1.791	1.00
265_L	269_I	1.786	1.00
57_A	61_G	1.770	1.00
91_I	95_L	1.770	1.00
257_L	261_D	1.767	1.00
61_G	65_L	1.761	1.00
90_A	94_L	1.745	1.00
263_G	267_Y	1.732	1.00
51_V	55_A	1.723	1.00
163_H	167_L	1.710	1.00
158_T	161_E	1.702	1.00
244_A	258_A	1.650	1.00
127_L	130_R	1.647	1.00
109_R	112_R	1.582	1.00
36_P	39_V	1.548	1.00
120_H	124_H	1.544	1.00
145_M	148_V	1.533	1.00
116_A	120_H	1.531	1.00
6_L	10_T	1.529	1.00
51_V	54_L	1.498	1.00
255_G	258_A	1.492	1.00
4_L	7_L	1.489	1.00
117_E	120_H	1.487	1.00
146_Y	149_G	1.478	1.00
121_L	124_H	1.464	1.00
74_V	77_V	1.436	1.00
156_F	160_T	1.433	1.00
249_L	254_W	1.411	1.00
138_L	141_H	1.411	1.00
268_V	271_G	1.396	1.00
255_G	259_A	1.378	1.00
119_E	123_A	1.377	1.00
156_F	159_A	1.371	1.00
239_L	243_L	1.365	1.00
71_L	75_G	1.362	1.00
235_G	239_L	1.351	1.00
72_H	75_G	1.349	1.00
118_L	121_L	1.341	1.00
225_G	229_T	1.329	1.00
104_F	108_R	1.323	1.00
227_S	231_A	1.318	1.00
221_M	225_G	1.317	1.00
14_R	18_D	1.305	1.00
117_E	121_L	1.302	1.00
264_L	268_V	1.300	1.00
226_L	229_T	1.297	1.00
135_L	138_L	1.287	1.00
226_L	233_L	1.285	1.00
97_L	225_G	1.283	1.00
20_D	23_K	1.279	1.00
119_E	122_L	1.275	1.00
78_I	82_V	1.274	1.00
89_I	271_G	1.269	1.00
75_G	78_I	1.268	1.00
252_G	255_G	1.266	1.00
106_R	112_R	1.262	1.00
250_S	255_G	1.258	1.00
128_H	134_P	1.253	1.00
87_L	91_I	1.242	1.00
203_M	207_Y	1.237	1.00
128_H	132_F	1.236	1.00
240_L	244_A	1.235	1.00
142_S	145_M	1.232	1.00
144_H	148_V	1.225	1.00
233_L	237_I	1.214	1.00
151_L	154_L	1.212	1.00
50_V	150_L	1.210	1.00
116_A	119_E	1.199	1.00
127_L	131_L	1.199	1.00
83_A	239_L	1.198	1.00
52_T	189_A	1.196	1.00
167_L	170_G	1.186	1.00
157_D	160_T	1.186	1.00
69_S	72_H	1.184	1.00
237_I	241_G	1.184	1.00
256_A	259_A	1.180	1.00
238_E	242_L	1.175	1.00
154_L	157_D	1.173	1.00
220_N	223_I	1.169	1.00
153_G	156_F	1.164	1.00
98_R	102_R	1.163	1.00
18_D	197_T	1.159	1.00
272_L	276_T	1.158	1.00
12_G	15_H	1.155	1.00
101_R	105_R	1.155	1.00
225_G	230_V	1.145	1.00
225_G	233_L	1.141	1.00
59_A	62_A	1.135	1.00
143_W	146_Y	1.131	1.00
218_Y	222_T	1.125	1.00
118_L	122_L	1.120	1.00
97_L	100_I	1.112	1.00
253_F	256_A	1.102	1.00
140_D	143_W	1.098	1.00
168_A	172_A	1.096	1.00
105_R	109_R	1.093	1.00
275_L	279_V	1.088	1.00
217_L	221_M	1.082	1.00
120_H	123_A	1.079	1.00
28_K	31_V	1.077	1.00
78_I	81_E	1.074	1.00
135_L	148_V	1.072	1.00
113_Y	118_L	1.068	1.00
264_L	267_Y	1.066	1.00
87_L	90_A	1.062	1.00
43_F	47_H	1.059	1.00
255_G	261_D	1.058	1.00
183_L	186_L	1.057	1.00
240_L	254_W	1.050	1.00
139_V	144_H	1.048	1.00
126_G	129_A	1.045	1.00
58_L	62_A	1.042	1.00
70_A	73_M	1.040	1.00
94_L	98_R	1.039	1.00
93_N	271_G	1.037	1.00
126_G	131_L	1.028	1.00
224_T	229_T	1.026	1.00
149_G	156_F	1.021	1.00
118_L	124_H	1.020	1.00
17_F	270_V	1.017	1.00
52_T	55_A	1.012	1.00
156_F	161_E	1.008	1.00
44_S	51_V	1.003	1.00
118_L	125_R	1.002	1.00
56_V	59_A	0.994	1.00
133_G	137_R	0.991	1.00
126_G	132_F	0.985	1.00
155_G	158_T	0.980	1.00
16_A	195_C	0.979	1.00
131_L	134_P	0.977	1.00
111_G	114_D	0.974	1.00
166_A	170_G	0.970	1.00
253_F	257_L	0.967	1.00
44_S	193_S	0.966	1.00
157_D	161_E	0.964	1.00
56_V	60_L	0.959	1.00
266_G	273_F	0.958	1.00
232_L	235_G	0.952	1.00
30_L	35_R	0.945	1.00
115_E	119_E	0.944	1.00
88_I	92_G	0.942	1.00
56_V	219_Y	0.941	1.00
260_L	265_L	0.939	1.00
113_Y	117_E	0.935	1.00
164_L	167_L	0.932	1.00
236_G	240_L	0.921	1.00
219_Y	222_T	0.919	1.00
37_L	234_I	0.910	1.00
136_F	139_V	0.908	1.00
166_A	181_I	0.905	1.00
96_V	100_I	0.903	1.00
119_E	125_R	0.903	1.00
137_R	140_D	0.900	1.00
113_Y	116_A	0.898	1.00
106_R	111_G	0.897	1.00
224_T	227_S	0.894	1.00
222_T	225_G	0.891	1.00
64_A	67_G	0.891	1.00
11_L	18_D	0.885	1.00
162_V	167_L	0.882	1.00
47_H	55_A	0.876	1.00
262_L	268_V	0.874	1.00
124_H	127_L	0.872	1.00
180_A	183_L	0.867	1.00
104_F	107_M	0.860	1.00
263_G	274_V	0.858	1.00
253_F	258_A	0.856	1.00
46_G	51_V	0.856	1.00
233_L	236_G	0.844	1.00
228_V	231_A	0.844	1.00
241_G	245_D	0.844	1.00
267_Y	274_V	0.842	1.00
178_F	182_L	0.841	1.00
144_H	147_P	0.835	1.00
266_G	277_W	0.834	1.00
226_L	230_V	0.834	1.00
77_V	81_E	0.832	1.00
30_L	36_P	0.829	1.00
121_L	125_R	0.828	1.00
93_N	97_L	0.824	1.00
129_A	132_F	0.822	1.00
40_G	47_H	0.822	1.00
230_V	269_I	0.822	1.00
195_C	205_A	0.822	1.00
7_L	11_L	0.821	1.00
256_A	260_L	0.821	1.00
68_L	71_L	0.819	1.00
73_M	77_V	0.819	1.00
170_G	173_A	0.817	1.00
61_G	64_A	0.816	1.00
63_L	66_L	0.804	1.00
214_G	218_Y	0.802	1.00
248_G	252_G	0.802	1.00
115_E	125_R	0.801	1.00
5_G	216_K	0.801	1.00
240_L	243_L	0.800	1.00
56_V	182_L	0.800	1.00
226_L	234_I	0.792	1.00
195_C	198_A	0.788	1.00
169_A	173_A	0.786	1.00
132_F	135_L	0.783	0.99
276_T	280_A	0.783	0.99
160_T	163_H	0.782	0.99
114_D	118_L	0.781	0.99
211_F	216_K	0.779	0.99
47_H	52_T	0.778	0.99
244_A	248_G	0.771	0.99
274_V	277_W	0.769	0.99
133_G	136_F	0.768	0.99
151_L	155_G	0.766	0.99
273_F	277_W	0.762	0.99
136_F	140_D	0.761	0.99
59_A	66_L	0.758	0.99
202_L	205_A	0.752	0.99
251_G	254_W	0.746	0.99
92_G	95_L	0.745	0.99
134_P	138_L	0.741	0.99
189_A	192_M	0.735	0.99
259_A	262_L	0.735	0.99
124_H	129_A	0.733	0.99
245_D	248_G	0.727	0.99
229_T	234_I	0.723	0.99
201_V	205_A	0.720	0.99
186_L	190_A	0.720	0.99
71_L	74_V	0.719	0.99
240_L	253_F	0.719	0.99
234_I	238_E	0.719	0.99
34_R	141_H	0.719	0.99
39_V	145_M	0.714	0.99
147_P	150_L	0.712	0.99
261_D	264_L	0.711	0.99
112_R	116_A	0.710	0.99
129_A	134_P	0.700	0.99
214_G	221_M	0.696	0.99
129_A	136_F	0.695	0.99
254_W	258_A	0.694	0.99
29_L	39_V	0.692	0.99
262_L	267_Y	0.690	0.99
202_L	212_A	0.689	0.99
94_L	232_L	0.686	0.99
167_L	171_A	0.682	0.99
257_L	260_L	0.682	0.99
70_A	74_V	0.682	0.99
238_E	241_G	0.681	0.99
62_A	65_L	0.680	0.99
125_R	129_A	0.677	0.99
134_P	137_R	0.673	0.98
88_I	95_L	0.671	0.98
114_D	122_L	0.671	0.98
5_G	9_Y	0.666	0.98
143_W	147_P	0.663	0.98
100_I	104_F	0.662	0.98
85_F	89_I	0.660	0.98
159_A	162_V	0.660	0.98
254_W	259_A	0.660	0.98
242_L	245_D	0.655	0.98
35_R	40_G	0.654	0.98
46_G	50_V	0.654	0.98
224_T	228_V	0.654	0.98
44_S	47_H	0.654	0.98
46_G	49_T	0.651	0.98
83_A	87_L	0.650	0.98
61_G	66_L	0.650	0.98
155_G	159_A	0.650	0.98
262_L	273_F	0.646	0.98
263_G	269_I	0.644	0.98
15_H	21_H	0.644	0.98
276_T	279_V	0.643	0.98
163_H	166_A	0.643	0.98
216_K	220_N	0.641	0.98
87_L	96_V	0.640	0.98
48_S	52_T	0.639	0.98
51_V	59_A	0.639	0.98
256_A	261_D	0.638	0.98
43_F	187_L	0.634	0.98
269_I	272_L	0.628	0.98
47_H	54_L	0.627	0.98
18_D	25_I	0.624	0.98
181_I	185_P	0.623	0.97
269_I	273_F	0.623	0.97
228_V	233_L	0.623	0.97
183_L	187_L	0.622	0.97
180_A	186_L	0.621	0.97
37_L	204_L	0.621	0.97
26_T	30_L	0.620	0.97
68_L	75_G	0.620	0.97
128_H	131_L	0.619	0.97
195_C	204_L	0.615	0.97
182_L	186_L	0.615	0.97
75_G	79_G	0.615	0.97
60_L	64_A	0.612	0.97
27_R	30_L	0.611	0.97
263_G	270_V	0.608	0.97
132_F	136_F	0.607	0.97
152_F	156_F	0.606	0.97
52_T	59_A	0.606	0.97
176_L	179_W	0.605	0.97
55_A	62_A	0.605	0.97
49_T	53_L	0.604	0.97
66_L	72_H	0.603	0.97
231_A	234_I	0.601	0.97
105_R	108_R	0.601	0.97
230_V	234_I	0.598	0.97
128_H	133_G	0.597	0.97
118_L	123_A	0.592	0.97
68_L	74_V	0.591	0.97
139_V	143_W	0.590	0.97
114_D	120_H	0.590	0.97
170_G	175_G	0.589	0.96
80_T	85_F	0.587	0.96
50_V	54_L	0.586	0.96
30_L	208_G	0.585	0.96
135_L	139_V	0.585	0.96
58_L	163_H	0.585	0.96
7_L	10_T	0.584	0.96
112_R	115_E	0.583	0.96
271_G	274_V	0.582	0.96
122_L	127_L	0.581	0.96
261_D	265_L	0.581	0.96
225_G	234_I	0.579	0.96
160_T	164_L	0.578	0.96
114_D	123_A	0.577	0.96
26_T	218_Y	0.574	0.96
76_G	80_T	0.573	0.96
44_S	55_A	0.573	0.96
20_D	24_A	0.572	0.96
72_H	78_I	0.572	0.96
79_G	82_V	0.572	0.96
244_A	249_L	0.571	0.96
176_L	182_L	0.568	0.96
146_Y	151_L	0.566	0.96
115_E	118_L	0.564	0.96
168_A	173_A	0.564	0.96
71_L	76_G	0.564	0.96
55_A	58_L	0.563	0.95
74_V	79_G	0.563	0.95
162_V	165_L	0.561	0.95
198_A	214_G	0.561	0.95
68_L	72_H	0.559	0.95
86_L	89_I	0.557	0.95
53_L	56_V	0.556	0.95
32_A	140_D	0.555	0.95
42_F	46_G	0.552	0.95
179_W	182_L	0.552	0.95
249_L	252_G	0.551	0.95
58_L	61_G	0.550	0.95
39_V	44_S	0.549	0.95
119_E	131_L	0.549	0.95
109_R	114_D	0.543	0.95
218_Y	221_M	0.541	0.94
245_D	250_S	0.541	0.94
268_V	275_L	0.541	0.94
55_A	166_A	0.541	0.94
73_M	76_G	0.540	0.94
115_E	122_L	0.539	0.94
221_M	226_L	0.536	0.94
206_A	211_F	0.531	0.94
245_D	249_L	0.531	0.94
252_G	256_A	0.528	0.94
76_G	79_G	0.525	0.94
127_L	132_F	0.523	0.93
50_V	53_L	0.523	0.93
231_A	235_G	0.522	0.93
126_G	134_P	0.522	0.93
265_L	268_V	0.520	0.93
158_T	162_V	0.520	0.93
253_F	260_L	0.519	0.93
6_L	9_Y	0.518	0.93
204_L	208_G	0.518	0.93
228_V	234_I	0.518	0.93
224_T	234_I	0.517	0.93
79_G	85_F	0.516	0.93
30_L	33_G	0.516	0.93
130_R	133_G	0.515	0.93
107_M	217_L	0.512	0.93
161_E	166_A	0.511	0.93
103_V	107_M	0.510	0.93
40_G	43_F	0.510	0.93
106_R	109_R	0.509	0.92
50_V	187_L	0.506	0.92
234_I	237_I	0.506	0.92
19_P	23_K	0.502	0.92
224_T	233_L	0.502	0.92
87_L	239_L	0.501	0.92
95_L	99_G	0.500	0.92

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
4pypA	1	0.3227	26.9	0.94	Contact Map
2xq2A	2	0.3369	17.5	0.945	Contact Map
3wdoA	1	0.5426	14.5	0.947	Contact Map
2l9uA	2	0.1418	14.4	0.947	Contact Map
2kluA	1	0.2447	12.8	0.948	Contact Map
4k0jA	3	0.3369	12.8	0.948	Contact Map
4tphA	2	0.3227	9.4	0.951	Contact Map
2l2tA	2	0.156	8.3	0.953	Contact Map
2f93B	2	0.1702	7.5	0.954	Contact Map
4tkrA	2	0.4681	6.8	0.955	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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