SODF - ECOLI - GREMLIN Contacts

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SODF - Superoxide dismutase [Fe]

UniProt:	P0AGD3	Sequences: MSFELPALPYAKDALAPHISAETIEYHYGKHHQTYVTNLNNLIKGTAFEGKSLEEIIRSSEGGVFNNAAQVWNHTFYWNCLAPNAGGEPTGKVAEAIAASFGSFADFKAQFTDAAIKNFGSGWTWLVKNSDGKLAIVSTSNAGTPLTTDATPLLTVDVWEHAYYIDYRNARPGYLEHFWALVNWEFVAKNLAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10954
Length:	193 (189)
Sequences:	4168 (2333)
Seq/√Len:	169.7

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
33_Q	37_T	4.031	1.00
170_A	173_G	2.891	1.00
106_D	109_A	2.529	1.00
94_A	98_A	2.514	1.00
186_F	189_K	2.494	1.00
129_N	135_A	2.418	1.00
22_E	168_R	2.364	1.00
115_A	124_T	2.334	1.00
38_N	41_N	2.319	1.00
21_A	25_E	2.318	1.00
93_V	188_A	2.269	1.00
186_F	190_N	2.230	1.00
156_V	175_L	2.180	1.00
18_H	180_A	2.077	1.00
109_A	113_D	2.048	1.00
95_E	98_A	2.005	1.00
81_L	178_F	1.924	1.00
118_N	138_S	1.911	1.00
100_S	133_K	1.908	1.00
112_T	176_E	1.867	1.00
106_D	110_Q	1.857	1.00
20_S	166_D	1.849	1.00
12_K	29_G	1.844	1.00
79_N	186_F	1.829	1.00
19_I	77_Y	1.823	1.00
173_G	176_E	1.814	1.00
96_A	99_A	1.789	1.00
115_A	156_V	1.777	1.00
36_V	71_V	1.761	1.00
96_A	191_L	1.702	1.00
115_A	175_L	1.677	1.00
113_D	117_K	1.668	1.00
154_L	187_V	1.667	1.00
4_E	7_A	1.623	1.00
110_Q	113_D	1.614	1.00
127_V	137_V	1.611	1.00
13_D	21_A	1.606	1.00
41_N	44_K	1.580	1.00
39_L	68_A	1.574	1.00
37_T	41_N	1.531	1.00
96_A	100_S	1.528	1.00
6_P	75_T	1.524	1.00
107_F	111_F	1.496	1.00
51_K	59_S	1.480	1.00
165_I	168_R	1.443	1.00
80_C	187_V	1.413	1.00
71_V	75_T	1.394	1.00
32_H	78_W	1.389	1.00
112_T	116_I	1.386	1.00
156_V	178_F	1.377	1.00
116_I	172_P	1.374	1.00
116_I	175_L	1.360	1.00
167_Y	177_H	1.334	1.00
128_K	191_L	1.331	1.00
82_A	85_A	1.330	1.00
24_I	77_Y	1.307	1.00
45_G	49_E	1.307	1.00
22_E	25_E	1.302	1.00
92_K	95_E	1.290	1.00
43_I	46_T	1.280	1.00
125_W	139_T	1.273	1.00
127_V	135_A	1.265	1.00
52_S	55_E	1.263	1.00
112_T	175_L	1.259	1.00
124_T	138_S	1.256	1.00
11_A	14_A	1.242	1.00
25_E	29_G	1.233	1.00
88_E	105_A	1.215	1.00
182_V	187_V	1.211	1.00
26_Y	168_R	1.207	1.00
112_T	179_W	1.202	1.00
80_C	186_F	1.202	1.00
38_N	67_N	1.192	1.00
5_L	28_Y	1.191	1.00
129_N	150_A	1.181	1.00
79_N	190_N	1.179	1.00
39_L	64_V	1.177	1.00
118_N	124_T	1.173	1.00
135_A	150_A	1.168	1.00
12_K	25_E	1.146	1.00
185_E	188_A	1.139	1.00
153_L	187_V	1.137	1.00
114_A	136_I	1.119	1.00
111_F	156_V	1.117	1.00
72_W	76_F	1.116	1.00
179_W	182_V	1.111	1.00
158_V	171_R	1.095	1.00
104_F	107_F	1.089	1.00
114_A	124_T	1.088	1.00
12_K	28_Y	1.078	1.00
3_F	39_L	1.076	1.00
69_A	142_A	1.074	1.00
72_W	144_T	1.072	1.00
183_N	186_F	1.069	1.00
9_P	79_N	1.057	0.99
109_A	176_E	1.057	0.99
90_T	188_A	1.055	0.99
77_Y	174_Y	1.053	0.99
34_T	38_N	1.052	0.99
163_Y	171_R	1.050	0.99
46_T	49_E	1.048	0.99
75_T	79_N	1.046	0.99
103_S	106_D	1.040	0.99
31_H	164_Y	1.032	0.99
97_I	107_F	1.022	0.99
80_C	190_N	1.021	0.99
3_F	43_I	1.020	0.99
95_E	99_A	1.016	0.99
65_F	143_G	0.991	0.99
178_F	182_V	0.980	0.99
107_F	136_I	0.974	0.99
20_S	23_T	0.967	0.99
92_K	188_A	0.964	0.99
76_F	186_F	0.963	0.99
111_F	178_F	0.962	0.99
177_H	180_A	0.948	0.99
32_H	75_T	0.945	0.99
113_D	116_I	0.942	0.99
127_V	150_A	0.935	0.99
23_T	166_D	0.934	0.99
82_A	86_G	0.934	0.99
105_A	108_K	0.928	0.99
154_L	182_V	0.926	0.99
114_A	138_S	0.920	0.99
185_E	189_K	0.907	0.98
137_V	150_A	0.906	0.98
173_G	177_H	0.889	0.98
47_A	51_K	0.885	0.98
36_V	40_N	0.884	0.98
88_E	98_A	0.880	0.98
22_E	166_D	0.878	0.98
70_Q	142_A	0.872	0.98
97_I	104_F	0.871	0.98
88_E	94_A	0.867	0.98
66_N	119_F	0.862	0.98
48_F	51_K	0.857	0.98
12_K	21_A	0.853	0.98
81_L	181_L	0.852	0.98
93_V	191_L	0.851	0.98
77_Y	156_V	0.848	0.98
104_F	108_K	0.844	0.97
110_Q	114_A	0.841	0.97
91_G	95_E	0.834	0.97
13_D	16_A	0.810	0.97
100_S	134_L	0.808	0.97
72_W	146_L	0.808	0.97
53_L	72_W	0.808	0.97
118_N	140_S	0.804	0.97
10_Y	81_L	0.803	0.97
128_K	132_G	0.803	0.97
129_N	133_K	0.803	0.97
3_F	56_I	0.803	0.97
96_A	128_K	0.798	0.96
93_V	97_I	0.795	0.96
93_V	187_V	0.788	0.96
30_K	170_A	0.787	0.96
29_G	33_Q	0.786	0.96
22_E	26_Y	0.785	0.96
34_T	37_T	0.782	0.96
6_P	32_H	0.779	0.96
82_A	185_E	0.767	0.96
71_V	78_W	0.766	0.96
44_K	49_E	0.761	0.95
51_K	55_E	0.753	0.95
124_T	156_V	0.751	0.95
89_P	104_F	0.746	0.95
12_K	24_I	0.743	0.95
30_K	33_Q	0.729	0.94
128_K	153_L	0.728	0.94
99_A	133_K	0.725	0.94
128_K	151_T	0.725	0.94
16_A	21_A	0.714	0.94
74_H	157_D	0.712	0.93
89_P	94_A	0.711	0.93
82_A	183_N	0.707	0.93
32_H	71_V	0.707	0.93
108_K	176_E	0.691	0.92
108_K	112_T	0.691	0.92
108_K	180_A	0.689	0.92
62_G	65_F	0.687	0.92
18_H	177_H	0.683	0.92
88_E	108_K	0.682	0.92
101_F	110_Q	0.681	0.92
105_A	109_A	0.678	0.92
82_A	87_G	0.677	0.92
19_I	24_I	0.677	0.92
73_N	125_W	0.677	0.92
48_F	53_L	0.676	0.92
184_W	187_V	0.675	0.92
27_H	74_H	0.674	0.92
5_L	32_H	0.674	0.92
7_A	11_A	0.669	0.91
33_Q	36_V	0.668	0.91
125_W	155_T	0.666	0.91
41_N	45_G	0.664	0.91
34_T	116_I	0.650	0.90
155_T	174_Y	0.650	0.90
39_L	53_L	0.649	0.90
24_I	174_Y	0.645	0.90
94_A	104_F	0.644	0.90
19_I	174_Y	0.644	0.90
108_K	179_W	0.641	0.89
76_F	190_N	0.640	0.89
121_S	141_N	0.640	0.89
137_V	148_T	0.639	0.89
98_A	103_S	0.636	0.89
90_T	185_E	0.628	0.88
38_N	63_G	0.627	0.88
90_T	94_A	0.626	0.88
137_V	147_T	0.626	0.88
30_K	169_N	0.625	0.88
142_A	155_T	0.623	0.88
91_G	94_A	0.622	0.88
48_F	61_E	0.621	0.88
45_G	56_I	0.621	0.88
167_Y	173_G	0.620	0.88
84_N	87_G	0.614	0.87
27_H	157_D	0.613	0.87
55_E	59_S	0.612	0.87
35_Y	70_Q	0.611	0.87
126_L	134_L	0.607	0.87
118_N	136_I	0.605	0.86
18_H	181_L	0.603	0.86
5_L	33_Q	0.603	0.86
55_E	58_R	0.599	0.86
60_S	147_T	0.599	0.86
36_V	75_T	0.597	0.86
19_I	81_L	0.596	0.86
144_T	147_T	0.596	0.86
9_P	183_N	0.596	0.86
65_F	142_A	0.595	0.86
101_F	134_L	0.590	0.85
74_H	161_H	0.589	0.85
157_D	161_H	0.587	0.85
143_G	148_T	0.586	0.85
110_Q	136_I	0.584	0.85
31_H	169_N	0.584	0.85
175_L	179_W	0.584	0.85
124_T	158_V	0.584	0.85
122_G	158_V	0.578	0.84
56_I	59_S	0.576	0.84
54_E	72_W	0.575	0.84
117_K	138_S	0.572	0.83
92_K	191_L	0.572	0.83
53_L	60_S	0.569	0.83
114_A	118_N	0.568	0.83
164_Y	169_N	0.568	0.83
18_H	178_F	0.567	0.83
69_A	73_N	0.563	0.82
39_L	43_I	0.562	0.82
147_T	150_A	0.562	0.82
26_Y	29_G	0.562	0.82
65_F	70_Q	0.561	0.82
172_P	176_E	0.561	0.82
115_A	158_V	0.561	0.82
73_N	142_A	0.558	0.82
90_T	104_F	0.551	0.81
18_H	166_D	0.549	0.81
80_C	153_L	0.549	0.81
7_A	29_G	0.548	0.81
16_A	22_E	0.547	0.81
91_G	188_A	0.547	0.81
20_S	26_Y	0.545	0.80
27_H	161_H	0.544	0.80
111_F	136_I	0.540	0.80
42_L	64_V	0.538	0.79
90_T	93_V	0.537	0.79
104_F	179_W	0.530	0.78
100_S	135_A	0.529	0.78
26_Y	165_I	0.528	0.78
118_N	141_N	0.527	0.78
91_G	104_F	0.527	0.78
89_P	188_A	0.526	0.78
166_D	181_L	0.521	0.77
71_V	77_Y	0.521	0.77
100_S	191_L	0.518	0.77
157_D	160_E	0.516	0.77
26_Y	30_K	0.516	0.77
5_L	36_V	0.515	0.76
60_S	65_F	0.509	0.76
19_I	23_T	0.506	0.75
22_E	165_I	0.504	0.75
128_K	133_K	0.502	0.75
54_E	58_R	0.500	0.74

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
3tqjA	2	0.9948	100	-0.012	Contact Map
1mngA	3	0.9741	100	-0.012	Contact Map
1gv3A	2	1	100	-0.01	Contact Map
1uerA	2	0.9896	100	-0.01	Contact Map
2awpA	2	1	100	-0.01	Contact Map
4yetA	2	1	100	-0.01	Contact Map
2cw2A	2	0.9948	100	-0.008	Contact Map
2rcvA	2	0.9896	100	-0.007	Contact Map
5a9gA	2	1	100	-0.006	Contact Map
2nybA	2	0.9948	100	-0.003	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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