HEM4 - ECOLI - GREMLIN Contacts

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HEM4 - Uroporphyrinogen-III synthase

UniProt:	P09126	Sequences: MSILVTRPSPAGEELVSRLRTLGQVAWHFPLIEFSPGQQLPQLADQLAALGESDLLFALSQHAVAFAQSQLHQQDRKWPRLPDYFAIGRTTALALHTVSGQKILYPQDREISEVLLQLPELQNIAGKRALILRGNGGRELIGDTLTARGAEVTFCECYQRCAIHYDGAEEAMRWQAREVTMVVVTSGEMLQQLWSLIPQWYREHWLLHCRLLVVSERLAKLARELGWQDIKVADNADNDALLRALQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10430
Length:	246 (234)
Sequences:	3959 (3093)
Seq/√Len:	202.2

ECOLI - HEM4
BACSU - HEM4 YJJA NASF
HALSA - Q9HMY3
SULSO - Q980U3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_L	24_Q	4.434	1.00
213_V	219_A	3.922	1.00
53_S	153_T	3.683	1.00
135_N	159_Q	3.423	1.00
187_G	221_L	3.103	1.00
128_R	151_E	2.545	1.00
55_L	85_F	2.545	1.00
219_A	232_V	2.541	1.00
133_R	154_F	2.470	1.00
53_S	130_L	2.440	1.00
191_Q	221_L	2.429	1.00
181_M	212_L	2.418	1.00
144_T	147_A	2.373	1.00
35_S	161_C	2.343	1.00
18_R	22_L	2.163	1.00
35_S	159_Q	2.120	1.00
44_A	70_Q	2.113	1.00
86_A	92_A	2.106	1.00
190_L	222_A	2.049	1.00
68_Q	98_V	2.033	1.00
54_D	127_K	2.010	1.00
33_E	163_I	1.997	1.00
163_I	192_Q	1.982	1.00
116_L	144_T	1.956	1.00
58_A	64_V	1.911	1.00
18_R	239_D	1.911	1.00
213_V	222_A	1.867	1.00
211_L	227_W	1.841	1.00
65_A	94_A	1.807	1.00
133_R	137_G	1.797	1.00
84_Y	100_G	1.796	1.00
219_A	223_R	1.722	1.00
16_V	28_H	1.711	1.00
34_F	160_R	1.692	1.00
194_W	225_L	1.666	1.00
104_L	118_L	1.656	1.00
220_K	223_R	1.653	1.00
233_A	240_A	1.643	1.00
111_I	114_V	1.628	1.00
55_L	83_D	1.622	1.00
213_V	232_V	1.613	1.00
94_A	97_T	1.602	1.00
124_I	127_K	1.591	1.00
112_S	141_I	1.587	1.00
36_P	66_F	1.585	1.00
55_L	129_A	1.584	1.00
11_A	62_H	1.578	1.00
113_E	138_R	1.570	1.00
77_K	81_L	1.569	1.00
58_A	67_A	1.561	1.00
220_K	224_E	1.560	1.00
184_V	193_L	1.552	1.00
5_V	16_V	1.540	1.00
16_V	26_A	1.537	1.00
34_F	62_H	1.530	1.00
128_R	153_T	1.519	1.00
191_Q	225_L	1.518	1.00
185_T	189_M	1.510	1.00
139_E	143_D	1.502	1.00
85_F	115_L	1.483	1.00
5_V	12_G	1.467	1.00
236_A	240_A	1.460	1.00
120_E	148_R	1.436	1.00
142_G	146_T	1.415	1.00
235_N	240_A	1.399	1.00
222_A	229_D	1.394	1.00
4_L	179_V	1.389	1.00
66_F	157_C	1.384	1.00
221_L	224_E	1.381	1.00
214_V	218_L	1.380	1.00
184_V	190_L	1.370	1.00
211_L	222_A	1.356	1.00
143_D	146_T	1.342	1.00
61_Q	90_T	1.319	1.00
107_Q	118_L	1.317	1.00
212_L	231_K	1.315	1.00
142_G	154_F	1.308	1.00
135_N	156_E	1.301	1.00
54_D	128_R	1.289	1.00
17_S	21_T	1.285	1.00
17_S	20_R	1.279	1.00
124_I	150_A	1.271	1.00
92_A	96_H	1.264	1.00
215_S	218_L	1.263	1.00
33_E	161_C	1.254	1.00
162_A	195_S	1.254	1.00
222_A	227_W	1.254	1.00
183_V	241_L	1.237	1.00
16_V	20_R	1.225	1.00
49_A	52_E	1.225	1.00
212_L	241_L	1.222	1.00
181_M	210_R	1.218	1.00
20_R	26_A	1.195	1.00
86_A	105_Y	1.191	1.00
52_E	128_R	1.185	1.00
237_D	240_A	1.171	1.00
19_L	26_A	1.156	1.00
160_R	188_E	1.154	1.00
221_L	225_L	1.153	1.00
184_V	211_L	1.132	1.00
113_E	140_L	1.123	1.00
162_A	192_Q	1.097	1.00
31_L	192_Q	1.079	1.00
79_P	82_P	1.079	1.00
56_L	84_Y	1.073	1.00
187_G	217_R	1.072	1.00
92_A	105_Y	1.068	1.00
131_I	142_G	1.062	1.00
194_W	227_W	1.057	1.00
13_E	28_H	1.047	1.00
104_L	115_L	1.047	1.00
45_D	49_A	1.047	1.00
231_K	244_A	1.040	1.00
129_A	150_A	1.036	1.00
123_N	127_K	1.030	1.00
216_E	236_A	1.021	1.00
5_V	19_L	1.013	1.00
210_R	231_K	1.006	1.00
56_L	132_L	1.005	1.00
64_V	94_A	1.002	1.00
137_G	154_F	0.995	1.00
140_L	144_T	0.988	1.00
64_V	91_T	0.984	1.00
168_A	172_M	0.981	1.00
3_I	181_M	0.978	1.00
27_W	179_V	0.977	1.00
18_R	21_T	0.963	0.99
112_S	140_L	0.958	0.99
49_A	153_T	0.954	0.99
187_G	218_L	0.949	0.99
96_H	101_Q	0.946	0.99
77_K	80_R	0.945	0.99
136_G	188_E	0.944	0.99
57_F	119_P	0.936	0.99
55_L	104_L	0.935	0.99
216_E	220_K	0.922	0.99
31_L	196_L	0.915	0.99
9_S	12_G	0.906	0.99
37_G	159_Q	0.906	0.99
89_R	110_E	0.904	0.99
65_A	97_T	0.895	0.99
116_L	148_R	0.891	0.99
86_A	95_L	0.891	0.99
9_S	13_E	0.888	0.99
87_I	112_S	0.886	0.99
144_T	148_R	0.873	0.99
61_Q	94_A	0.873	0.99
32_I	160_R	0.856	0.99
112_S	160_R	0.854	0.99
136_G	160_R	0.850	0.99
93_L	97_T	0.841	0.99
212_L	244_A	0.840	0.99
183_V	212_L	0.829	0.98
34_F	66_F	0.829	0.98
111_I	216_E	0.823	0.98
7_R	10_P	0.822	0.98
62_H	66_F	0.820	0.98
58_A	132_L	0.820	0.98
185_T	238_N	0.819	0.98
43_L	157_C	0.818	0.98
146_T	152_V	0.816	0.98
57_F	115_L	0.816	0.98
131_I	141_I	0.815	0.98
130_L	155_C	0.815	0.98
172_M	176_A	0.810	0.98
37_G	156_E	0.806	0.98
45_D	48_A	0.806	0.98
104_L	120_E	0.805	0.98
222_A	226_G	0.804	0.98
126_G	150_A	0.802	0.98
83_D	103_I	0.800	0.98
112_S	116_L	0.798	0.98
63_A	131_I	0.795	0.98
132_L	157_C	0.795	0.98
12_G	28_H	0.793	0.98
69_S	98_V	0.790	0.98
67_A	132_L	0.789	0.98
211_L	230_I	0.788	0.98
138_R	217_R	0.782	0.98
173_R	178_E	0.780	0.98
15_L	183_V	0.778	0.98
182_V	209_C	0.778	0.98
5_V	26_A	0.777	0.98
171_A	175_Q	0.775	0.98
86_A	102_K	0.775	0.98
96_H	102_K	0.773	0.98
233_A	244_A	0.762	0.97
234_D	243_R	0.762	0.97
65_A	69_S	0.761	0.97
192_Q	196_L	0.760	0.97
62_H	65_A	0.757	0.97
15_L	19_L	0.756	0.97
106_P	110_E	0.752	0.97
90_T	93_L	0.752	0.97
223_R	228_Q	0.752	0.97
7_R	189_M	0.750	0.97
120_E	144_T	0.748	0.97
108_D	114_V	0.745	0.97
5_V	28_H	0.742	0.97
94_A	98_V	0.739	0.97
5_V	183_V	0.737	0.97
116_L	140_L	0.732	0.97
63_A	132_L	0.731	0.97
165_Y	196_L	0.729	0.96
87_I	115_L	0.728	0.96
33_E	164_H	0.726	0.96
66_F	69_S	0.726	0.96
5_V	10_P	0.725	0.96
143_D	147_A	0.724	0.96
58_A	84_Y	0.724	0.96
188_E	215_S	0.723	0.96
233_A	236_A	0.720	0.96
112_S	137_G	0.719	0.96
198_P	201_Y	0.715	0.96
134_G	156_E	0.715	0.96
108_D	111_I	0.715	0.96
223_R	232_V	0.714	0.96
32_I	192_Q	0.714	0.96
115_L	119_P	0.707	0.96
13_E	17_S	0.707	0.96
110_E	237_D	0.706	0.96
31_L	193_L	0.705	0.96
131_I	152_V	0.704	0.96
32_I	186_S	0.699	0.96
55_L	119_P	0.694	0.95
57_F	141_I	0.692	0.95
42_Q	45_D	0.691	0.95
110_E	236_A	0.691	0.95
67_A	157_C	0.687	0.95
134_G	157_C	0.686	0.95
44_A	48_A	0.684	0.95
116_L	119_P	0.682	0.95
7_R	11_A	0.677	0.95
110_E	114_V	0.677	0.95
111_I	217_R	0.675	0.95
133_R	156_E	0.662	0.94
210_R	230_I	0.660	0.94
216_E	232_V	0.659	0.94
111_I	236_A	0.658	0.94
85_F	185_T	0.658	0.94
56_L	130_L	0.654	0.94
9_S	28_H	0.652	0.94
112_S	217_R	0.648	0.93
15_L	185_T	0.647	0.93
48_A	74_Q	0.647	0.93
87_I	91_T	0.647	0.93
121_L	148_R	0.646	0.93
8_P	34_F	0.643	0.93
190_L	225_L	0.639	0.93
117_Q	144_T	0.638	0.93
133_R	139_E	0.636	0.93
93_L	96_H	0.636	0.93
145_L	150_A	0.635	0.93
191_Q	224_E	0.634	0.93
136_G	156_E	0.634	0.93
100_G	103_I	0.634	0.93
85_F	104_L	0.628	0.92
217_R	236_A	0.627	0.92
146_T	151_E	0.626	0.92
118_L	122_Q	0.621	0.92
77_K	82_P	0.619	0.92
32_I	188_E	0.619	0.92
133_R	142_G	0.616	0.92
169_E	173_R	0.613	0.91
42_Q	46_Q	0.606	0.91
3_I	6_T	0.604	0.91
240_A	244_A	0.603	0.91
114_V	117_Q	0.599	0.90
29_F	165_Y	0.596	0.90
134_G	188_E	0.594	0.90
137_G	160_R	0.593	0.90
132_L	155_C	0.593	0.90
36_P	69_S	0.592	0.90
139_E	154_F	0.591	0.90
85_F	106_P	0.590	0.90
29_F	167_G	0.590	0.90
43_L	70_Q	0.589	0.90
116_L	141_I	0.585	0.89
132_L	137_G	0.584	0.89
57_F	85_F	0.581	0.89
191_Q	195_S	0.581	0.89
123_N	150_A	0.579	0.89
183_V	242_L	0.578	0.89
131_I	154_F	0.578	0.89
131_I	137_G	0.577	0.89
39_Q	42_Q	0.577	0.89
12_G	16_V	0.576	0.89
138_R	160_R	0.574	0.88
95_L	100_G	0.573	0.88
44_A	74_Q	0.572	0.88
23_G	26_A	0.569	0.88
9_S	15_L	0.567	0.88
184_V	189_M	0.567	0.88
21_T	73_Q	0.565	0.88
58_A	131_I	0.564	0.88
163_I	166_D	0.564	0.88
87_I	134_G	0.564	0.88
131_I	185_T	0.562	0.87
27_W	173_R	0.558	0.87
137_G	217_R	0.557	0.87
182_V	211_L	0.557	0.87
88_G	91_T	0.557	0.87
112_S	138_R	0.556	0.87
181_M	231_K	0.554	0.87
99_S	102_K	0.553	0.87
116_L	120_E	0.551	0.86
57_F	145_L	0.551	0.86
70_Q	73_Q	0.548	0.86
134_G	160_R	0.546	0.86
166_D	169_E	0.544	0.86
58_A	86_A	0.544	0.86
18_R	242_L	0.543	0.86
112_S	188_E	0.540	0.85
206_L	209_C	0.537	0.85
46_Q	153_T	0.536	0.85
57_F	150_A	0.535	0.85
119_P	122_Q	0.535	0.85
44_A	73_Q	0.533	0.84
55_L	118_L	0.533	0.84
32_I	189_M	0.529	0.84
11_A	61_Q	0.529	0.84
89_R	237_D	0.526	0.84
59_L	160_R	0.524	0.83
41_P	45_D	0.523	0.83
6_T	15_L	0.523	0.83
140_L	143_D	0.522	0.83
20_R	25_V	0.522	0.83
55_L	127_K	0.521	0.83
240_A	243_R	0.517	0.83
119_P	148_R	0.517	0.83
63_A	160_R	0.517	0.83
60_S	91_T	0.515	0.82
14_E	17_S	0.514	0.82
86_A	91_T	0.513	0.82
85_F	118_L	0.513	0.82
13_E	66_F	0.512	0.82
34_F	61_Q	0.511	0.82
190_L	213_V	0.510	0.82
235_N	243_R	0.509	0.82
223_R	229_D	0.508	0.82
103_I	106_P	0.507	0.81
8_P	11_A	0.507	0.81
19_L	22_L	0.507	0.81
47_L	50_L	0.505	0.81
63_A	137_G	0.504	0.81
160_R	192_Q	0.503	0.81
58_A	91_T	0.502	0.81
31_L	163_I	0.502	0.81
139_E	142_G	0.500	0.81
136_G	191_Q	0.500	0.81
211_L	229_D	0.500	0.81

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
3re1A	1	0.9837	100	0.12	Contact Map
3mw8A	1	0.9512	100	0.142	Contact Map
3d8tA	1	0.9675	100	0.142	Contact Map
4es6A	1	0.9797	100	0.143	Contact Map
1wcwA	1	0.9675	100	0.145	Contact Map
1jr2A	1	0.9797	100	0.145	Contact Map
3p9zA	1	0.8374	100	0.246	Contact Map
2fepA	2	0.9309	96.2	0.879	Contact Map
3gv0A	2	0.9309	96.1	0.88	Contact Map
3qk7A	2	0.9187	96.1	0.88	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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