SODM2 - HALSA - GREMLIN Contacts

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SODM2 - Superoxide dismutase [Mn] 2

UniProt:	P09224	Sequences: MSQHELPSLPYDYDALEPHISEQVVTWHHDTHHQSYVDGLNSAEETLAENRETGDHASTAGALGDVTHNGCGHYLHTMFWEHMSPDGGGEPSGALADRIAADFGSYENWRAEFEVAAGAASGWALLVYDPVAKQLRNVAVDNHDEGALWGSHPILALDVWEHSYYYDYGPDRGSFVDAFFEVIDWDPIAANYDDVVSLFE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (190)
Sequences:	4207 (2406)
Seq/√Len:	174.5

ECOLI - SODF SODM
BACSU - SODF SODM
HALSA - SODM2 SODM1
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_D	4.084	1.00
171_D	174_S	3.001	1.00
108_N	111_A	2.599	1.00
96_A	100_A	2.570	1.00
187_P	190_A	2.521	1.00
129_D	136_R	2.398	1.00
23_Q	169_G	2.386	1.00
117_A	124_A	2.354	1.00
39_G	42_S	2.331	1.00
95_L	189_A	2.267	1.00
22_E	26_T	2.258	1.00
157_L	176_V	2.251	1.00
187_P	191_N	2.211	1.00
111_A	115_V	2.144	1.00
97_D	100_A	2.056	1.00
102_D	134_Q	1.951	1.00
83_M	179_F	1.927	1.00
114_E	177_D	1.920	1.00
108_N	112_E	1.892	1.00
13_Y	30_D	1.885	1.00
21_S	167_D	1.862	1.00
117_A	157_L	1.833	1.00
81_E	187_P	1.826	1.00
20_I	79_F	1.819	1.00
98_R	101_A	1.809	1.00
37_V	73_H	1.784	1.00
174_S	177_D	1.774	1.00
19_H	181_E	1.736	1.00
98_R	192_Y	1.717	1.00
117_A	176_V	1.712	1.00
155_L	188_I	1.683	1.00
42_S	45_E	1.670	1.00
115_V	119_A	1.653	1.00
127_V	138_V	1.651	1.00
112_E	115_V	1.621	1.00
60_A	63_L	1.598	1.00
5_E	8_S	1.593	1.00
98_R	102_D	1.588	1.00
189_A	193_D	1.581	1.00
14_D	22_E	1.569	1.00
40_L	70_G	1.552	1.00
38_D	42_S	1.540	1.00
7_P	77_T	1.539	1.00
94_A	193_D	1.538	1.00
109_W	113_F	1.518	1.00
166_Y	169_G	1.494	1.00
157_L	179_F	1.436	1.00
82_H	188_I	1.425	1.00
73_H	77_T	1.424	1.00
114_E	118_G	1.408	1.00
33_H	80_W	1.400	1.00
52_E	55_D	1.390	1.00
118_G	173_G	1.383	1.00
124_A	139_A	1.379	1.00
168_Y	178_A	1.350	1.00
118_G	176_V	1.317	1.00
25_V	79_F	1.312	1.00
127_V	136_R	1.307	1.00
125_L	140_V	1.305	1.00
84_S	87_G	1.303	1.00
90_E	107_E	1.281	1.00
23_Q	26_T	1.280	1.00
94_A	97_D	1.272	1.00
128_Y	192_Y	1.262	1.00
12_D	15_A	1.253	1.00
114_E	176_V	1.244	1.00
183_I	188_I	1.229	1.00
82_H	187_P	1.222	1.00
190_A	194_D	1.221	1.00
6_L	29_H	1.220	1.00
26_T	30_D	1.218	1.00
27_W	169_G	1.216	1.00
40_L	66_V	1.206	1.00
39_G	69_N	1.204	1.00
114_E	180_F	1.199	1.00
136_R	151_S	1.197	1.00
129_D	151_S	1.196	1.00
116_A	124_A	1.166	1.00
186_D	189_A	1.158	1.00
81_E	191_N	1.147	1.00
159_V	172_R	1.142	1.00
13_Y	26_T	1.138	1.00
164_Y	172_R	1.134	1.00
180_F	183_I	1.132	1.00
154_I	188_I	1.127	1.00
13_Y	29_H	1.119	1.00
90_E	96_A	1.109	1.00
116_A	137_N	1.108	1.00
74_Y	145_E	1.103	1.00
71_C	143_H	1.090	1.00
106_Y	109_W	1.085	1.00
105_S	108_N	1.084	1.00
113_F	157_L	1.084	1.00
4_H	40_L	1.077	1.00
74_Y	78_M	1.077	1.00
67_T	144_D	1.074	1.00
10_P	81_E	1.071	1.00
111_A	177_D	1.066	1.00
32_H	165_Y	1.064	1.00
184_D	187_P	1.056	1.00
94_A	189_A	1.056	1.00
92_S	189_A	1.050	1.00
46_T	49_E	1.041	0.99
82_H	191_N	1.039	0.99
79_F	175_F	1.036	0.99
35_S	39_G	1.030	0.99
4_H	44_E	1.024	0.99
77_T	81_E	1.014	0.99
90_E	100_A	1.008	0.99
97_D	101_A	1.006	0.99
115_V	118_G	0.999	0.99
179_F	183_I	0.998	0.99
78_M	187_P	0.987	0.99
51_R	59_T	0.977	0.99
116_A	139_A	0.975	0.99
113_F	179_F	0.972	0.99
99_I	109_W	0.970	0.99
109_W	137_N	0.968	0.99
21_S	24_V	0.968	0.99
107_E	110_R	0.952	0.99
131_V	134_Q	0.948	0.99
127_V	151_S	0.948	0.99
51_R	55_D	0.942	0.99
155_L	183_I	0.929	0.99
138_V	151_S	0.926	0.99
24_V	167_D	0.923	0.99
174_S	178_A	0.918	0.99
13_Y	22_E	0.914	0.99
33_H	77_T	0.899	0.98
84_S	88_G	0.883	0.98
37_V	41_N	0.878	0.98
98_R	128_Y	0.872	0.98
186_D	190_A	0.872	0.98
79_F	157_L	0.872	0.98
110_R	181_E	0.864	0.98
102_D	135_L	0.863	0.98
83_M	182_V	0.861	0.98
72_G	143_H	0.859	0.98
14_D	17_E	0.854	0.98
53_T	74_Y	0.851	0.98
93_G	97_D	0.849	0.98
23_Q	167_D	0.842	0.98
35_S	38_D	0.838	0.98
95_L	188_I	0.833	0.98
23_Q	27_W	0.832	0.97
106_Y	110_R	0.830	0.97
112_E	116_A	0.825	0.97
95_L	192_Y	0.818	0.97
74_Y	147_A	0.803	0.97
99_I	106_Y	0.797	0.97
84_S	186_D	0.795	0.97
31_T	171_D	0.789	0.97
124_A	157_L	0.785	0.96
95_L	99_I	0.773	0.96
7_P	33_H	0.772	0.96
128_Y	154_I	0.768	0.96
129_D	134_Q	0.767	0.96
177_D	181_E	0.759	0.96
30_D	34_Q	0.757	0.96
11_Y	83_M	0.756	0.96
4_H	56_H	0.753	0.96
73_H	80_W	0.751	0.95
6_L	33_H	0.745	0.95
64_G	67_T	0.735	0.95
84_S	184_D	0.731	0.95
76_H	158_D	0.721	0.94
101_A	134_Q	0.721	0.94
110_R	114_E	0.720	0.94
178_A	181_E	0.716	0.94
78_M	191_N	0.715	0.94
55_D	58_S	0.712	0.94
86_D	89_G	0.711	0.94
33_H	73_H	0.709	0.94
17_E	22_E	0.703	0.94
91_P	96_A	0.701	0.93
90_E	110_R	0.697	0.93
128_Y	152_H	0.693	0.93
35_S	118_G	0.689	0.93
13_Y	25_V	0.687	0.93
103_F	112_E	0.681	0.92
31_T	34_Q	0.681	0.92
110_R	177_D	0.679	0.92
91_P	106_Y	0.675	0.92
107_E	111_A	0.675	0.92
110_R	180_F	0.673	0.92
121_S	142_N	0.672	0.92
19_H	178_A	0.670	0.92
49_E	53_T	0.665	0.92
40_L	53_T	0.663	0.91
20_I	175_F	0.662	0.91
145_E	148_L	0.661	0.91
128_Y	132_A	0.656	0.91
20_I	25_V	0.655	0.91
75_L	125_L	0.652	0.91
96_A	106_Y	0.648	0.90
34_Q	37_V	0.648	0.90
28_H	76_H	0.646	0.90
125_L	156_A	0.641	0.90
84_S	89_G	0.641	0.90
92_S	186_D	0.641	0.90
31_T	170_P	0.638	0.90
37_V	77_T	0.637	0.90
39_G	65_D	0.633	0.89
67_T	143_H	0.628	0.89
25_V	175_F	0.628	0.89
8_S	12_D	0.627	0.89
138_V	148_L	0.624	0.89
185_W	188_I	0.623	0.89
156_A	175_F	0.623	0.89
20_I	83_M	0.622	0.89
122_G	159_V	0.620	0.88
100_A	105_S	0.619	0.88
124_A	159_V	0.614	0.88
36_Y	72_G	0.614	0.88
48_A	51_R	0.611	0.88
47_L	59_T	0.610	0.88
119_A	139_A	0.608	0.88
28_H	158_D	0.604	0.87
6_L	34_Q	0.603	0.87
19_H	182_V	0.601	0.87
6_L	37_V	0.600	0.87
93_G	106_Y	0.597	0.87
93_G	96_A	0.596	0.86
44_E	56_H	0.595	0.86
168_Y	174_S	0.594	0.86
10_P	184_D	0.589	0.86
143_H	156_A	0.579	0.85
21_S	27_W	0.577	0.85
103_F	135_L	0.576	0.85
19_H	179_F	0.571	0.84
67_T	72_G	0.571	0.84
19_H	167_D	0.571	0.84
173_G	177_D	0.570	0.84
92_S	96_A	0.570	0.84
32_H	170_P	0.570	0.84
76_H	162_H	0.570	0.84
44_E	48_A	0.569	0.84
165_Y	170_P	0.566	0.84
102_D	136_R	0.566	0.84
17_E	23_Q	0.565	0.83
71_C	75_L	0.560	0.83
158_D	162_H	0.559	0.83
27_W	171_D	0.554	0.82
43_A	65_D	0.553	0.82
40_L	56_H	0.553	0.82
129_D	132_A	0.551	0.82
106_Y	180_F	0.549	0.82
112_E	137_N	0.549	0.82
126_L	135_L	0.548	0.82
40_L	44_E	0.547	0.81
82_H	154_I	0.545	0.81
50_N	54_G	0.545	0.81
176_V	180_F	0.544	0.81
45_E	49_E	0.544	0.81
148_L	151_S	0.543	0.81
117_A	159_V	0.542	0.81
27_W	166_Y	0.540	0.81
113_F	137_N	0.540	0.81
27_W	30_D	0.539	0.80
8_S	30_D	0.538	0.80
28_H	162_H	0.537	0.80
87_G	93_G	0.533	0.80
43_A	66_V	0.533	0.80
190_A	193_D	0.532	0.80
191_N	194_D	0.531	0.80
92_S	106_Y	0.530	0.79
93_G	189_A	0.529	0.79
75_L	143_H	0.526	0.79
73_H	79_F	0.525	0.79
102_D	192_Y	0.522	0.78
27_W	31_T	0.522	0.78
144_D	149_W	0.521	0.78
37_V	53_T	0.520	0.78
167_D	182_V	0.514	0.77
92_S	95_L	0.514	0.77
79_F	156_A	0.513	0.77
47_L	61_G	0.508	0.76
141_D	144_D	0.507	0.76
171_D	177_D	0.507	0.76
4_H	53_T	0.506	0.76
147_A	153_P	0.505	0.76
42_S	46_T	0.505	0.76
20_I	24_V	0.502	0.76
4_H	74_Y	0.502	0.76
31_T	174_S	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	0.035	Contact Map
3ak2A	4	0.995	100	0.041	Contact Map
2rcvA	2	0.955	100	0.044	Contact Map
1gv3A	2	0.97	100	0.044	Contact Map
1mngA	3	0.94	100	0.045	Contact Map
1dt0A	2	0.97	100	0.046	Contact Map
4h3eA	1	0.98	100	0.046	Contact Map
1b06A	4	0.99	100	0.047	Contact Map
1pl4A	4	0.97	100	0.048	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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