SODM1 - HALSA - GREMLIN Contacts

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SODM1 - Superoxide dismutase [Mn] 1

UniProt:	P09737	Sequences: MSEYELPPLPYDYDALEPHISEQVLTWHHDTHHQGYVNGWNDAEETLAENRETGDHASTAGALGDVTHNGSGHILHTLFWQSMSPAGGDEPSGALADRIAADFGSYENWRAEFEAAASAASGWALLVYDSHSNTLRNVAVDNHDEGALWGSHPILALDVWEHSYYYDYGPDRGSFVDAFFEVVDWDEPTERFEQAAERFE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (190)
Sequences:	4209 (2412)
Seq/√Len:	175.0

ECOLI - SODF SODM
BACSU - SODF SODM
HALSA - SODM1 SODM2
SULSO - SODF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_Q	38_N	4.037	1.00
171_D	174_S	2.936	1.00
108_N	111_A	2.568	1.00
96_A	100_A	2.526	1.00
187_E	190_E	2.469	1.00
129_D	136_R	2.381	1.00
23_Q	169_G	2.348	1.00
117_A	124_A	2.331	1.00
39_G	42_D	2.287	1.00
95_L	189_T	2.236	1.00
22_E	26_T	2.224	1.00
157_L	176_V	2.199	1.00
187_E	191_R	2.190	1.00
111_A	115_A	2.082	1.00
97_D	100_A	2.002	1.00
83_M	179_F	1.922	1.00
102_D	134_T	1.919	1.00
114_E	177_D	1.891	1.00
13_Y	30_D	1.858	1.00
21_S	167_D	1.855	1.00
108_N	112_E	1.850	1.00
81_Q	187_E	1.824	1.00
117_A	157_L	1.787	1.00
174_S	177_D	1.787	1.00
98_R	101_A	1.774	1.00
37_V	73_H	1.762	1.00
20_I	79_F	1.759	1.00
98_R	192_F	1.725	1.00
19_H	181_E	1.707	1.00
117_A	176_V	1.692	1.00
155_L	188_P	1.676	1.00
115_A	119_A	1.623	1.00
42_D	45_E	1.611	1.00
127_V	138_V	1.606	1.00
112_E	115_A	1.600	1.00
5_E	8_P	1.599	1.00
14_D	22_E	1.574	1.00
189_T	193_E	1.570	1.00
38_N	42_D	1.558	1.00
40_W	70_G	1.557	1.00
94_A	193_E	1.551	1.00
98_R	102_D	1.546	1.00
60_A	63_L	1.540	1.00
7_P	77_T	1.526	1.00
109_W	113_F	1.498	1.00
166_Y	169_G	1.495	1.00
157_L	179_F	1.434	1.00
82_S	188_P	1.411	1.00
33_H	80_W	1.403	1.00
118_S	173_G	1.388	1.00
52_E	55_D	1.382	1.00
114_E	118_S	1.375	1.00
73_H	77_T	1.362	1.00
124_A	139_A	1.358	1.00
168_Y	178_A	1.347	1.00
84_S	87_G	1.335	1.00
125_L	140_V	1.316	1.00
94_A	97_D	1.306	1.00
23_Q	26_T	1.285	1.00
25_L	79_F	1.284	1.00
118_S	176_V	1.279	1.00
90_E	107_E	1.271	1.00
127_V	136_R	1.258	1.00
51_R	59_T	1.254	1.00
128_Y	192_F	1.253	1.00
12_D	15_A	1.242	1.00
114_E	176_V	1.232	1.00
129_D	151_S	1.225	1.00
27_W	169_G	1.218	1.00
26_T	30_D	1.209	1.00
82_S	187_E	1.208	1.00
39_G	69_N	1.207	1.00
6_L	29_H	1.201	1.00
114_E	180_F	1.194	1.00
40_W	66_V	1.193	1.00
183_V	188_P	1.191	1.00
190_E	194_Q	1.185	1.00
136_R	151_S	1.180	1.00
81_Q	191_R	1.168	1.00
116_A	124_A	1.166	1.00
159_V	172_R	1.160	1.00
164_Y	172_R	1.156	1.00
186_D	189_T	1.151	1.00
13_Y	29_H	1.135	1.00
13_Y	26_T	1.135	1.00
154_I	188_P	1.122	1.00
71_S	143_H	1.106	1.00
74_I	145_E	1.105	1.00
180_F	183_V	1.102	1.00
4_Y	40_W	1.098	1.00
113_F	157_L	1.098	1.00
116_A	137_N	1.094	1.00
90_E	96_A	1.093	1.00
105_S	108_N	1.091	1.00
184_D	187_E	1.080	1.00
10_P	81_Q	1.073	1.00
74_I	78_L	1.072	1.00
106_Y	109_W	1.069	1.00
94_A	189_T	1.066	1.00
111_A	177_D	1.061	1.00
82_S	191_R	1.055	1.00
67_T	144_D	1.050	1.00
32_H	165_Y	1.036	0.99
4_Y	44_E	1.034	0.99
77_T	81_Q	1.032	0.99
35_G	39_G	1.032	0.99
92_S	189_T	1.029	0.99
131_H	134_T	1.022	0.99
79_F	175_F	1.011	0.99
179_F	183_V	1.002	0.99
115_A	118_S	1.000	0.99
116_A	139_A	0.993	0.99
97_D	101_A	0.988	0.99
109_W	137_N	0.987	0.99
78_L	187_E	0.980	0.99
127_V	151_S	0.972	0.99
90_E	100_A	0.970	0.99
21_S	24_V	0.969	0.99
99_I	109_W	0.967	0.99
24_V	167_D	0.952	0.99
107_E	110_R	0.947	0.99
113_F	179_F	0.943	0.99
51_R	55_D	0.939	0.99
155_L	183_V	0.937	0.99
33_H	77_T	0.922	0.99
84_S	88_G	0.917	0.99
13_Y	22_E	0.910	0.99
174_S	178_A	0.905	0.99
138_V	151_S	0.899	0.99
37_V	41_N	0.896	0.98
110_R	181_E	0.891	0.98
72_G	143_H	0.890	0.98
186_D	190_E	0.875	0.98
98_R	128_Y	0.868	0.98
83_M	182_V	0.865	0.98
93_G	97_D	0.853	0.98
53_T	74_I	0.849	0.98
112_E	116_A	0.844	0.98
79_F	157_L	0.844	0.98
102_D	135_L	0.842	0.98
46_T	49_E	0.841	0.98
14_D	17_E	0.841	0.98
35_G	38_N	0.834	0.98
23_Q	167_D	0.830	0.97
99_I	106_Y	0.828	0.97
74_I	147_A	0.827	0.97
129_D	134_T	0.821	0.97
106_Y	110_R	0.819	0.97
95_L	188_P	0.819	0.97
95_L	192_F	0.814	0.97
128_Y	133_N	0.807	0.97
31_T	171_D	0.805	0.97
95_L	99_I	0.803	0.97
23_Q	27_W	0.801	0.97
84_S	186_D	0.799	0.97
44_E	48_A	0.790	0.97
124_A	157_L	0.788	0.97
7_P	33_H	0.786	0.97
128_Y	154_I	0.777	0.96
11_Y	83_M	0.765	0.96
73_H	80_W	0.760	0.96
45_E	49_E	0.757	0.96
30_D	34_Q	0.757	0.96
101_A	134_T	0.755	0.96
177_D	181_E	0.753	0.96
178_A	181_E	0.746	0.95
90_E	110_R	0.744	0.95
6_L	33_H	0.738	0.95
13_Y	25_L	0.732	0.95
76_H	158_D	0.731	0.95
84_S	184_D	0.728	0.95
64_G	67_T	0.726	0.95
86_A	89_D	0.725	0.95
49_E	53_T	0.722	0.94
148_L	151_S	0.716	0.94
110_R	114_E	0.711	0.94
33_H	73_H	0.708	0.94
17_E	22_E	0.706	0.94
20_I	175_F	0.704	0.94
31_T	34_Q	0.701	0.94
128_Y	152_H	0.699	0.93
4_Y	56_H	0.696	0.93
138_V	148_L	0.693	0.93
103_F	112_E	0.691	0.93
55_D	58_S	0.684	0.93
107_E	111_A	0.683	0.93
91_P	96_A	0.683	0.93
35_G	118_S	0.682	0.93
110_R	180_F	0.678	0.92
75_L	125_L	0.673	0.92
121_S	142_N	0.672	0.92
39_G	65_D	0.665	0.92
125_L	156_A	0.664	0.92
28_H	76_H	0.662	0.91
31_T	170_P	0.660	0.91
78_L	191_R	0.656	0.91
110_R	177_D	0.656	0.91
19_H	178_A	0.654	0.91
100_A	105_S	0.654	0.91
156_A	175_F	0.653	0.91
40_W	53_T	0.651	0.91
91_P	106_Y	0.648	0.91
122_G	159_V	0.648	0.91
185_W	188_P	0.646	0.90
92_S	186_D	0.644	0.90
20_I	25_L	0.643	0.90
145_E	148_L	0.638	0.90
37_V	77_T	0.636	0.90
20_I	83_M	0.635	0.90
25_L	175_F	0.631	0.89
67_T	143_H	0.630	0.89
36_Y	72_G	0.629	0.89
93_G	96_A	0.628	0.89
34_Q	37_V	0.628	0.89
47_L	59_T	0.628	0.89
84_S	89_D	0.628	0.89
6_L	37_V	0.624	0.89
44_E	56_H	0.622	0.89
165_Y	170_P	0.620	0.89
124_A	159_V	0.620	0.89
168_Y	174_S	0.618	0.88
8_P	12_D	0.614	0.88
96_A	106_Y	0.613	0.88
92_S	96_A	0.609	0.88
6_L	34_Q	0.605	0.87
19_H	182_V	0.604	0.87
28_H	158_D	0.598	0.87
119_A	139_A	0.596	0.87
67_T	72_G	0.594	0.86
32_H	170_P	0.590	0.86
93_G	106_Y	0.589	0.86
143_H	156_A	0.585	0.86
158_D	162_H	0.583	0.85
76_H	162_H	0.575	0.85
112_E	137_N	0.575	0.85
10_P	184_D	0.574	0.84
75_L	143_H	0.570	0.84
176_V	180_F	0.567	0.84
19_H	179_F	0.565	0.84
173_G	177_D	0.562	0.83
71_S	75_L	0.558	0.83
19_H	167_D	0.558	0.83
40_W	56_H	0.557	0.83
21_S	27_W	0.557	0.83
8_P	30_D	0.557	0.83
17_E	23_Q	0.554	0.82
102_D	136_R	0.551	0.82
43_A	65_D	0.551	0.82
43_A	66_V	0.550	0.82
106_Y	180_F	0.550	0.82
82_S	154_I	0.549	0.82
191_R	194_Q	0.549	0.82
117_A	159_V	0.544	0.81
28_H	162_H	0.543	0.81
48_A	51_R	0.543	0.81
27_W	30_D	0.541	0.81
130_S	133_N	0.540	0.81
190_E	193_E	0.538	0.80
27_W	166_Y	0.537	0.80
126_L	135_L	0.537	0.80
141_D	144_D	0.533	0.80
40_W	44_E	0.532	0.80
93_G	189_T	0.532	0.80
103_F	135_L	0.530	0.79
50_N	55_D	0.529	0.79
92_S	95_L	0.529	0.79
113_F	137_N	0.527	0.79
55_D	59_T	0.526	0.79
43_A	69_N	0.526	0.79
27_W	31_T	0.523	0.79
92_S	106_Y	0.522	0.78
79_F	156_A	0.522	0.78
171_D	177_D	0.519	0.78
20_I	24_V	0.517	0.78
130_S	134_T	0.517	0.78
102_D	192_F	0.513	0.77
44_E	49_E	0.511	0.77
46_T	50_N	0.510	0.77
144_D	149_W	0.506	0.76
4_Y	74_I	0.505	0.76
87_G	93_G	0.503	0.76
46_T	61_G	0.503	0.76
130_S	151_S	0.501	0.76
147_A	153_P	0.501	0.76
94_A	192_F	0.500	0.75

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
1xreA	2	0.96	100	0.032	Contact Map
1ma1A	4	0.98	100	0.034	Contact Map
3ak2A	4	0.995	100	0.039	Contact Map
1mngA	3	0.94	100	0.043	Contact Map
1gv3A	2	0.97	100	0.043	Contact Map
2rcvA	2	0.955	100	0.044	Contact Map
1b06A	4	0.99	100	0.044	Contact Map
4h3eA	1	0.98	100	0.045	Contact Map
1pl4A	4	0.97	100	0.045	Contact Map
1dt0A	2	0.97	100	0.046	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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