PDUO - BACSU - GREMLIN Contacts

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PDUO - Cob(I)yrinic acid a,c-diamide adenosyltransferase

UniProt:	O34899	Sequences: MKLYTKTGDKGQTGLVGGRTDKDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALMKSEEIHETVLRYLNRLSDYFFAAARVVNARSGIGDVEYERSAIVFRDRNSSES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	193 (175)
Sequences:	2452 (1584)
Seq/√Len:	119.8

BACSU - PDUO
HALSA - Q9HPN7
SULSO - Q7LXT1 Q980D7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_L	129_T	4.105	1.00
136_V	153_L	3.771	1.00
23_D	141_K	3.078	1.00
28_E	135_R	2.828	1.00
4_Y	98_D	2.778	1.00
14_G	19_R	2.741	1.00
39_F	124_I	2.561	1.00
40_I	60_L	2.539	1.00
43_A	122_L	2.431	1.00
23_D	138_A	2.401	1.00
87_E	91_S	2.377	1.00
44_L	57_T	2.347	1.00
46_E	117_K	2.301	1.00
39_F	128_I	2.255	1.00
27_V	30_Y	2.146	1.00
16_V	75_A	2.143	1.00
59_E	96_R	2.085	1.00
66_E	152_Y	2.015	1.00
40_I	160_F	2.003	1.00
59_E	159_Y	1.948	1.00
166_V	170_R	1.892	1.00
32_T	135_R	1.846	1.00
21_D	141_K	1.839	1.00
159_Y	163_A	1.814	1.00
66_E	89_S	1.790	1.00
87_E	148_T	1.780	1.00
117_K	121_L	1.766	1.00
7_T	14_G	1.751	1.00
59_E	100_Y	1.710	1.00
128_I	131_R	1.689	1.00
28_E	32_T	1.680	1.00
23_D	137_V	1.669	1.00
92_F	96_R	1.654	1.00
103_E	170_R	1.632	1.00
119_A	168_N	1.620	1.00
125_A	160_F	1.613	1.00
96_R	99_A	1.571	1.00
73_D	146_H	1.570	1.00
68_F	71_G	1.568	1.00
100_Y	159_Y	1.559	1.00
122_L	167_V	1.548	1.00
3_L	162_A	1.537	1.00
24_S	143_E	1.517	1.00
39_F	125_A	1.466	1.00
168_N	175_D	1.444	1.00
4_Y	94_E	1.409	1.00
135_R	138_A	1.397	1.00
90_V	148_T	1.394	1.00
35_E	131_R	1.383	1.00
91_S	95_T	1.363	1.00
139_L	143_E	1.342	1.00
116_S	171_S	1.342	1.00
56_L	163_A	1.338	1.00
74_L	136_V	1.337	1.00
56_L	167_V	1.305	1.00
37_N	68_F	1.296	1.00
13_T	27_V	1.288	1.00
20_T	24_S	1.267	1.00
42_L	124_I	1.235	0.99
46_E	121_L	1.233	0.99
101_T	162_A	1.224	0.99
38_S	127_T	1.217	0.99
42_L	121_L	1.193	0.99
62_T	92_F	1.192	0.99
87_E	151_R	1.187	0.99
85_L	89_S	1.180	0.99
12_Q	21_D	1.162	0.99
104_A	162_A	1.146	0.99
55_D	99_A	1.137	0.99
30_Y	74_L	1.135	0.99
43_A	125_A	1.129	0.99
121_L	124_I	1.125	0.99
100_Y	166_V	1.124	0.99
4_Y	97_I	1.118	0.99
39_F	121_L	1.103	0.99
116_S	168_N	1.097	0.99
29_S	136_V	1.096	0.99
45_A	117_K	1.096	0.99
108_K	177_E	1.085	0.98
45_A	120_S	1.079	0.98
43_A	167_V	1.058	0.98
21_D	24_S	1.051	0.98
96_R	159_Y	1.039	0.98
55_D	170_R	1.031	0.98
66_E	92_F	1.021	0.98
7_T	19_R	1.020	0.98
47_L	118_C	1.016	0.98
7_T	12_Q	1.013	0.98
39_F	43_A	1.010	0.98
118_C	167_V	0.998	0.97
63_I	152_Y	0.984	0.97
140_M	150_L	0.976	0.97
97_I	162_A	0.972	0.97
45_A	121_L	0.968	0.97
148_T	151_R	0.957	0.97
76_I	79_E	0.956	0.97
32_T	131_R	0.954	0.96
73_D	84_K	0.949	0.96
105_P	169_A	0.944	0.96
26_R	143_E	0.936	0.96
109_K	177_E	0.928	0.96
16_V	76_I	0.919	0.96
28_E	138_A	0.914	0.96
15_L	20_T	0.902	0.95
44_L	61_L	0.900	0.95
110_F	161_F	0.894	0.95
70_C	149_V	0.889	0.95
57_T	61_L	0.879	0.94
54_E	58_A	0.879	0.94
37_N	64_Q	0.877	0.94
34_D	126_R	0.873	0.94
37_N	71_G	0.869	0.94
119_A	175_D	0.867	0.94
14_G	18_G	0.862	0.94
24_S	142_S	0.861	0.94
59_E	99_A	0.861	0.94
33_I	67_L	0.854	0.94
136_V	149_V	0.851	0.93
169_A	174_G	0.850	0.93
41_G	64_Q	0.848	0.93
32_T	132_A	0.836	0.93
115_G	168_N	0.814	0.92
132_A	153_L	0.811	0.92
65_H	69_D	0.797	0.91
88_E	91_S	0.796	0.91
25_L	135_R	0.794	0.91
42_L	117_K	0.790	0.91
33_I	70_C	0.780	0.90
90_V	151_R	0.778	0.90
129_T	160_F	0.776	0.90
13_T	20_T	0.775	0.90
61_L	176_V	0.772	0.90
62_T	66_E	0.771	0.90
99_A	103_E	0.769	0.89
86_T	89_S	0.768	0.89
100_Y	163_A	0.758	0.89
10_K	14_G	0.756	0.89
32_T	128_I	0.756	0.89
96_R	100_Y	0.755	0.89
94_E	98_D	0.748	0.88
104_A	107_L	0.748	0.88
60_L	122_L	0.746	0.88
138_A	142_S	0.746	0.88
30_Y	127_T	0.741	0.88
36_L	125_A	0.738	0.87
10_K	147_E	0.736	0.87
140_M	145_I	0.734	0.87
7_T	10_K	0.728	0.87
124_I	128_I	0.725	0.87
43_A	121_L	0.721	0.86
59_E	92_F	0.721	0.86
62_T	96_R	0.717	0.86
25_L	142_S	0.717	0.86
6_K	91_S	0.716	0.86
158_D	165_R	0.715	0.86
101_T	104_A	0.707	0.85
94_E	97_I	0.699	0.84
29_S	135_R	0.699	0.84
116_S	173_I	0.694	0.84
26_R	30_Y	0.692	0.84
42_L	46_E	0.690	0.84
113_P	126_R	0.688	0.84
72_G	76_I	0.685	0.83
114_G	120_S	0.684	0.83
111_I	161_F	0.683	0.83
140_M	144_E	0.676	0.82
20_T	27_V	0.674	0.82
122_L	163_A	0.674	0.82
177_E	180_R	0.672	0.82
2_K	6_K	0.668	0.82
136_V	150_L	0.662	0.81
121_L	125_A	0.655	0.80
109_K	180_R	0.653	0.80
111_I	164_A	0.649	0.80
119_A	164_A	0.645	0.79
33_I	153_L	0.644	0.79
137_V	150_L	0.640	0.79
29_S	33_I	0.637	0.79
41_G	71_G	0.636	0.78
63_I	156_L	0.633	0.78
116_S	119_A	0.630	0.78
112_L	115_G	0.628	0.78
35_E	128_I	0.628	0.78
95_T	99_A	0.627	0.77
107_L	161_F	0.626	0.77
146_H	149_V	0.624	0.77
29_S	139_L	0.622	0.77
38_S	164_A	0.622	0.77
137_V	140_M	0.620	0.77
36_L	39_F	0.619	0.77
69_D	178_Y	0.618	0.76
47_L	167_V	0.617	0.76
64_Q	71_G	0.615	0.76
3_L	104_A	0.614	0.76
65_H	178_Y	0.614	0.76
103_E	166_V	0.612	0.76
13_T	26_R	0.611	0.76
116_S	175_D	0.610	0.76
21_D	137_V	0.608	0.75
71_G	115_G	0.601	0.74
10_K	19_R	0.601	0.74
37_N	115_G	0.597	0.74
25_L	29_S	0.595	0.74
2_K	7_T	0.593	0.74
8_G	11_G	0.592	0.73
161_F	168_N	0.590	0.73
99_A	102_A	0.588	0.73
56_L	100_Y	0.588	0.73
15_L	26_R	0.585	0.73
123_H	164_A	0.585	0.73
2_K	98_D	0.582	0.72
33_I	136_V	0.581	0.72
104_A	109_K	0.578	0.72
33_I	132_A	0.578	0.72
25_L	138_A	0.570	0.71
30_Y	98_D	0.569	0.70
6_K	87_E	0.569	0.70
37_N	113_P	0.569	0.70
55_D	103_E	0.569	0.70
78_T	144_E	0.564	0.70
129_T	156_L	0.563	0.70
169_A	173_I	0.559	0.69
123_H	165_R	0.558	0.69
63_I	100_Y	0.557	0.69
6_K	151_R	0.556	0.69
32_T	134_R	0.556	0.69
85_L	148_T	0.554	0.68
78_T	81_K	0.547	0.67
111_I	165_R	0.541	0.67
49_G	54_E	0.539	0.66
73_D	83_Y	0.539	0.66
86_T	92_F	0.539	0.66
61_L	65_H	0.537	0.66
139_L	144_E	0.536	0.66
68_F	178_Y	0.535	0.66
31_G	34_D	0.535	0.66
36_L	43_A	0.534	0.66
49_G	117_K	0.532	0.65
56_L	166_V	0.531	0.65
117_K	120_S	0.526	0.64
3_L	158_D	0.526	0.64
114_G	175_D	0.526	0.64
171_S	174_G	0.524	0.64
147_E	151_R	0.524	0.64
132_A	139_L	0.521	0.64
25_L	139_L	0.520	0.64
65_H	68_F	0.519	0.63
29_S	132_A	0.519	0.63
92_F	95_T	0.518	0.63
62_T	102_A	0.513	0.63
116_S	174_G	0.511	0.62
139_L	145_I	0.508	0.62
104_A	178_Y	0.507	0.62
111_I	175_D	0.506	0.62
55_D	58_A	0.505	0.61
98_D	158_D	0.505	0.61
119_A	122_L	0.505	0.61
4_Y	90_V	0.505	0.61
118_C	121_L	0.504	0.61
38_S	42_L	0.503	0.61
20_T	30_Y	0.502	0.61
33_I	74_L	0.500	0.61

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
1rtyA	3	0.9016	100	0.064	Contact Map
3ke4A	3	0.8912	100	0.077	Contact Map
2ah6A	3	0.8497	100	0.077	Contact Map
2nt8A	3	0.9171	100	0.091	Contact Map
3ci3A	3	0.9534	100	0.094	Contact Map
2idxA	3	0.9171	100	0.115	Contact Map
2zhyA	3	0.8808	100	0.116	Contact Map
2g2dA	3	0.7979	100	0.125	Contact Map
1wy1A	3	0.7565	100	0.131	Contact Map
1wozA	3	0.8187	100	0.138	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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