DCD - ECOLI - GREMLIN Contacts

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DCD - Deoxycytidine triphosphate deaminase

UniProt:	P28248	Sequences: MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVHVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYNRREDAKYRNQQGAVASRIDKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11418
Length:	193 (174)
Sequences:	1768 (757)
Seq/√Len:	57.4

ECOLI - DCD
HALSA - DCD DUT
SULSO - DCD Q97UQ2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_T	132_S	5.073	1.00
45_R	71_D	4.504	1.00
35_V	156_G	3.804	1.00
10_A	14_E	3.773	1.00
127_I	135_I	3.514	1.00
36_R	94_L	3.326	1.00
19_I	33_V	3.156	1.00
40_K	72_E	3.049	1.00
102_D	162_P	2.781	1.00
11_W	16_R	2.588	1.00
94_L	152_G	2.293	1.00
111_S	115_R	2.265	1.00
38_G	92_V	2.113	1.00
118_L	147_L	2.107	1.00
39_N	74_V	2.051	1.00
27_R	36_R	2.031	1.00
105_G	160_F	1.980	1.00
7_D	165_G	1.939	1.00
96_S	132_S	1.901	1.00
44_F	90_L	1.796	0.99
15_G	18_S	1.777	0.99
106_W	161_E	1.741	0.99
22_R	33_V	1.731	0.99
55_S	150_R	1.708	0.99
9_E	24_P	1.670	0.99
12_L	22_R	1.649	0.99
92_V	134_C	1.637	0.99
125_H	128_D	1.635	0.99
7_D	164_S	1.629	0.99
23_P	26_E	1.621	0.99
53_D	150_R	1.612	0.99
31_A	129_P	1.579	0.98
94_L	151_P	1.557	0.98
11_W	103_L	1.501	0.98
3_L	7_D	1.500	0.98
99_L	105_G	1.483	0.98
7_D	10_A	1.470	0.97
84_H	87_E	1.462	0.97
22_R	28_I	1.458	0.97
132_S	181_N	1.442	0.97
172_N	177_A	1.426	0.97
34_D	110_R	1.420	0.97
115_R	157_A	1.398	0.97
112_S	188_S	1.387	0.96
93_T	137_L	1.378	0.96
99_L	103_L	1.375	0.96
29_N	157_A	1.364	0.96
35_V	158_L	1.352	0.96
28_I	33_V	1.351	0.96
23_P	36_R	1.350	0.96
35_V	97_V	1.346	0.96
6_R	168_V	1.342	0.96
38_G	152_G	1.324	0.95
4_C	7_D	1.320	0.95
9_E	168_V	1.317	0.95
89_A	141_N	1.315	0.95
111_S	157_A	1.285	0.94
134_C	184_G	1.276	0.94
127_I	158_L	1.265	0.94
80_A	150_R	1.239	0.93
113_L	153_M	1.230	0.93
80_A	148_A	1.208	0.92
84_H	146_P	1.202	0.92
27_R	154_L	1.201	0.92
120_V	156_G	1.197	0.92
2_R	161_E	1.188	0.92
8_I	33_V	1.177	0.91
122_V	146_P	1.174	0.91
138_E	182_Q	1.173	0.91
131_W	182_Q	1.144	0.90
41_F	81_F	1.133	0.90
11_W	100_P	1.115	0.89
40_K	92_V	1.113	0.89
114_A	138_E	1.066	0.87
110_R	133_G	1.060	0.86
101_A	170_P	1.059	0.86
20_N	96_S	1.053	0.86
29_N	34_D	1.045	0.86
119_M	140_Y	1.045	0.86
73_I	81_F	1.037	0.85
18_S	98_T	1.037	0.85
100_P	103_L	1.019	0.84
39_N	76_D	1.001	0.83
91_A	109_G	0.992	0.83
167_A	170_P	0.984	0.82
53_D	146_P	0.979	0.82
108_D	121_H	0.977	0.82
42_R	72_E	0.975	0.81
10_A	18_S	0.975	0.81
9_E	28_I	0.974	0.81
35_V	93_T	0.963	0.81
109_G	114_A	0.960	0.80
7_D	11_W	0.935	0.79
105_G	127_I	0.932	0.78
8_I	16_R	0.931	0.78
109_G	121_H	0.912	0.77
82_Y	158_L	0.911	0.77
110_R	157_A	0.895	0.76
112_S	157_A	0.889	0.75
8_I	160_F	0.882	0.74
110_R	154_L	0.877	0.74
114_A	121_H	0.873	0.74
4_C	164_S	0.871	0.74
93_T	155_I	0.871	0.74
101_A	166_P	0.862	0.73
109_G	182_Q	0.861	0.73
10_A	13_D	0.857	0.72
23_P	27_R	0.855	0.72
100_P	133_G	0.852	0.72
59_D	184_G	0.850	0.72
114_A	124_A	0.849	0.72
106_W	126_R	0.847	0.71
4_C	165_G	0.847	0.71
85_P	118_L	0.844	0.71
102_D	166_P	0.840	0.71
34_D	159_S	0.839	0.71
118_L	139_F	0.827	0.70
131_W	135_I	0.826	0.70
126_R	131_W	0.822	0.69
128_D	131_W	0.819	0.69
11_W	102_D	0.818	0.69
118_L	141_N	0.803	0.67
28_I	172_N	0.801	0.67
90_L	136_V	0.799	0.67
101_A	130_G	0.796	0.67
54_L	153_M	0.796	0.67
16_R	102_D	0.783	0.65
45_R	59_D	0.781	0.65
107_L	127_I	0.779	0.65
4_C	163_L	0.765	0.64
12_L	33_V	0.754	0.62
32_T	124_A	0.751	0.62
108_D	138_E	0.749	0.62
17_L	160_F	0.746	0.62
128_D	179_Y	0.746	0.62
81_F	89_A	0.746	0.62
125_H	131_W	0.740	0.61
53_D	148_A	0.731	0.60
31_A	141_N	0.729	0.60
100_P	160_F	0.725	0.59
141_N	147_L	0.718	0.59
110_R	115_R	0.717	0.59
24_P	158_L	0.712	0.58
16_R	98_T	0.708	0.58
9_E	13_D	0.708	0.58
122_V	158_L	0.706	0.57
173_R	177_A	0.703	0.57
3_L	162_P	0.701	0.57
11_W	160_F	0.696	0.56
93_T	114_A	0.694	0.56
104_V	126_R	0.687	0.55
41_F	91_A	0.683	0.55
18_S	96_S	0.682	0.55
9_E	39_N	0.682	0.55
101_A	160_F	0.681	0.55
186_V	189_R	0.680	0.55
14_E	79_E	0.679	0.54
37_L	149_L	0.678	0.54
23_P	137_L	0.672	0.54
85_P	146_P	0.663	0.53
91_A	139_F	0.662	0.53
3_L	11_W	0.661	0.52
11_W	17_L	0.659	0.52
59_D	71_D	0.658	0.52
139_F	185_A	0.658	0.52
87_E	154_L	0.658	0.52
40_K	74_V	0.658	0.52
110_R	178_K	0.658	0.52
82_Y	148_A	0.657	0.52
76_D	79_E	0.655	0.52
36_R	95_E	0.646	0.51
118_L	140_Y	0.641	0.50
76_D	80_A	0.639	0.50
37_L	91_A	0.639	0.50
13_D	24_P	0.635	0.50
75_L	80_A	0.634	0.50
9_E	183_Q	0.633	0.49
78_G	169_R	0.632	0.49
11_W	15_G	0.627	0.49
90_L	118_L	0.623	0.48
113_L	149_L	0.623	0.48
119_M	142_S	0.622	0.48
24_P	35_V	0.619	0.48
48_T	71_D	0.617	0.48
9_E	12_L	0.616	0.48
93_T	135_I	0.615	0.47
105_G	135_I	0.614	0.47
93_T	109_G	0.614	0.47
31_A	114_A	0.614	0.47
123_T	131_W	0.611	0.47
137_L	155_I	0.610	0.47
75_L	181_N	0.609	0.47
115_R	133_G	0.607	0.47
121_H	125_H	0.606	0.46
180_R	184_G	0.605	0.46
45_R	83_L	0.596	0.45
105_G	158_L	0.594	0.45
146_P	156_G	0.594	0.45
42_R	93_T	0.590	0.45
9_E	14_E	0.589	0.45
148_A	151_P	0.589	0.45
121_H	124_A	0.589	0.45
172_N	180_R	0.585	0.44
34_D	154_L	0.584	0.44
51_F	82_Y	0.584	0.44
2_R	159_S	0.584	0.44
41_F	75_L	0.580	0.44
12_L	20_N	0.578	0.43
83_L	156_G	0.578	0.43
163_L	167_A	0.577	0.43
81_F	84_H	0.576	0.43
70_S	146_P	0.576	0.43
14_E	21_P	0.575	0.43
30_G	109_G	0.573	0.43
88_L	140_Y	0.569	0.42
2_R	49_A	0.569	0.42
35_V	135_I	0.568	0.42
85_P	144_K	0.566	0.42
32_T	157_A	0.562	0.42
104_V	142_S	0.560	0.41
6_R	10_A	0.559	0.41
34_D	133_G	0.557	0.41
97_V	158_L	0.555	0.41
114_A	177_A	0.554	0.41
133_G	182_Q	0.554	0.41
29_N	111_S	0.553	0.41
33_V	160_F	0.551	0.41
83_L	139_F	0.550	0.40
35_V	155_I	0.546	0.40
111_S	133_G	0.544	0.40
41_F	151_P	0.543	0.40
82_Y	150_R	0.541	0.39
13_D	16_R	0.541	0.39
90_L	137_L	0.541	0.39
108_D	131_W	0.540	0.39
116_L	188_S	0.538	0.39
29_N	112_S	0.538	0.39
24_P	71_D	0.537	0.39
42_R	81_F	0.535	0.39
2_R	104_V	0.535	0.39
42_R	70_S	0.535	0.39
13_D	22_R	0.535	0.39
134_C	183_Q	0.531	0.38
109_G	119_M	0.529	0.38
118_L	126_R	0.522	0.37
81_F	107_L	0.521	0.37
124_A	128_D	0.520	0.37
133_G	157_A	0.519	0.37
30_G	114_A	0.517	0.37
173_R	187_A	0.516	0.37
29_N	110_R	0.513	0.37
104_V	159_S	0.511	0.36
31_A	167_A	0.508	0.36
105_G	129_P	0.508	0.36
108_D	125_H	0.507	0.36
51_F	166_P	0.505	0.36
101_A	173_R	0.504	0.36
105_G	131_W	0.503	0.36
139_F	149_L	0.502	0.35
114_A	136_V	0.500	0.35
6_R	14_E	0.500	0.35

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
1xs1A	5	1	100	0.172	Contact Map
2qxxA	3	0.9534	100	0.202	Contact Map
1pkhA	5	0.8756	100	0.223	Contact Map
4xjcA	3	0.9067	100	0.242	Contact Map
4dhkA	5	0.8135	100	0.278	Contact Map
3km3A	4	0.7668	100	0.278	Contact Map
2r9qA	4	0.8549	100	0.28	Contact Map
2yzjA	3	0.8187	100	0.33	Contact Map
3lqwA	3	0.6425	99.9	0.626	Contact Map
1f7dA	3	0.5907	99.8	0.64	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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