DCD - HALSA - GREMLIN Contacts

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DCD - Probable deoxycytidine triphosphate deaminase

UniProt:	Q9HSG3	Sequences: MILSDQDILARLADGDLAIEPLEDVDLQVQPASVDVRLGRRFLEFERANVPCIHPNREDEVDEYVTETVVEDGDEFILHPGDFVLGTTKERVEVPRDLVAQVEGRSSLGRLAVVVHATAGFIDPGFNGRVTLELSNLGKVPVALTPEMRISQLVFTELTSPADRPYGDERGSKYQDQDGPQASRIRGDREFGGTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	195 (174)
Sequences:	1827 (800)
Seq/√Len:	60.6

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
93_E	127_N	5.152	1.00
46_E	66_T	4.098	1.00
10_A	14_D	3.937	1.00
36_V	151_S	3.661	1.00
122_I	130_V	3.536	1.00
37_R	89_K	3.289	1.00
97_D	157_E	3.047	1.00
19_I	34_V	2.694	1.00
89_K	147_E	2.325	1.00
106_S	110_R	2.310	1.00
113_V	142_V	2.149	1.00
9_L	163_D	2.092	1.00
100_A	155_F	2.039	1.00
7_D	160_S	1.975	1.00
9_L	24_D	1.938	1.00
41_R	67_E	1.922	1.00
28_Q	37_R	1.917	1.00
7_D	159_T	1.907	1.00
39_G	87_T	1.883	1.00
91_R	127_N	1.838	1.00
94_V	100_A	1.804	1.00
11_R	16_D	1.720	0.99
101_Q	156_T	1.717	0.99
22_L	29_V	1.704	0.99
11_R	15_G	1.689	0.99
87_T	129_R	1.688	0.99
107_S	183_S	1.668	0.99
45_F	85_L	1.655	0.99
22_L	34_V	1.605	0.99
11_R	98_L	1.588	0.99
54_H	145_T	1.576	0.99
120_G	123_D	1.538	0.98
36_V	92_V	1.525	0.98
7_D	10_A	1.515	0.98
3_L	7_D	1.499	0.98
41_R	69_V	1.495	0.98
110_R	152_Q	1.478	0.98
30_Q	152_Q	1.463	0.98
127_N	176_D	1.436	0.98
79_H	82_D	1.433	0.98
75_E	143_A	1.432	0.98
29_V	34_V	1.427	0.97
122_I	153_L	1.418	0.97
32_A	124_P	1.417	0.97
108_L	148_M	1.415	0.97
40_R	69_V	1.413	0.97
94_V	98_L	1.399	0.97
36_V	153_L	1.380	0.97
109_G	133_E	1.364	0.97
88_T	132_L	1.362	0.97
4_S	7_D	1.339	0.96
35_D	105_R	1.337	0.96
106_S	152_Q	1.337	0.96
39_G	147_E	1.330	0.96
56_N	145_T	1.325	0.96
89_K	146_P	1.310	0.96
15_G	18_A	1.300	0.96
129_R	179_G	1.277	0.95
126_F	177_Q	1.265	0.95
167_G	172_S	1.256	0.95
84_V	136_N	1.255	0.95
12_L	22_L	1.242	0.94
114_V	135_S	1.215	0.94
2_I	156_T	1.195	0.93
42_F	76_F	1.188	0.93
11_R	95_P	1.184	0.93
133_E	177_Q	1.164	0.92
7_D	11_R	1.160	0.92
20_E	91_R	1.131	0.91
97_D	161_P	1.121	0.91
43_L	67_E	1.118	0.90
23_E	37_R	1.118	0.90
105_R	128_G	1.114	0.90
96_R	165_P	1.104	0.90
8_I	34_V	1.100	0.90
95_P	98_L	1.095	0.90
115_V	151_S	1.080	0.89
80_P	113_V	1.076	0.89
79_H	141_P	1.073	0.89
4_S	160_S	1.064	0.88
117_A	141_P	1.064	0.88
100_A	122_I	1.031	0.86
11_R	97_D	1.008	0.85
30_Q	35_D	1.006	0.85
9_L	29_V	1.006	0.85
18_A	93_E	0.978	0.83
107_S	152_Q	0.975	0.83
11_R	17_L	0.972	0.83
41_R	87_T	0.967	0.83
8_I	155_F	0.967	0.83
86_G	104_G	0.960	0.82
68_T	76_F	0.958	0.82
75_E	145_T	0.958	0.82
85_L	131_T	0.952	0.82
105_R	149_R	0.934	0.81
6_Q	163_D	0.931	0.80
77_I	143_A	0.928	0.80
95_P	128_G	0.920	0.79
35_D	154_V	0.915	0.79
109_G	119_A	0.901	0.78
96_R	161_P	0.895	0.78
105_R	152_Q	0.894	0.78
28_Q	149_R	0.894	0.78
31_P	152_Q	0.886	0.77
23_E	28_Q	0.885	0.77
104_G	177_Q	0.883	0.77
88_T	150_I	0.883	0.77
16_D	97_D	0.882	0.77
114_V	137_L	0.879	0.76
14_D	25_V	0.871	0.76
104_G	109_G	0.869	0.75
3_L	157_E	0.864	0.75
8_I	16_D	0.862	0.75
113_V	136_N	0.860	0.75
55_P	148_M	0.859	0.75
126_F	130_V	0.854	0.74
36_V	88_T	0.854	0.74
10_A	18_A	0.843	0.73
103_E	133_E	0.836	0.73
24_D	153_L	0.834	0.72
109_G	116_H	0.824	0.72
162_A	165_P	0.824	0.72
40_R	73_G	0.820	0.71
105_R	110_R	0.814	0.71
116_H	120_G	0.806	0.70
102_V	122_I	0.803	0.70
101_Q	121_F	0.789	0.68
123_D	174_Y	0.780	0.67
134_L	180_P	0.771	0.66
4_S	158_L	0.768	0.66
86_G	134_L	0.761	0.65
2_I	154_V	0.760	0.65
96_R	125_G	0.760	0.65
123_D	126_F	0.757	0.65
10_A	13_A	0.756	0.65
121_F	126_F	0.749	0.64
103_E	116_H	0.748	0.64
71_E	75_E	0.748	0.64
23_E	132_L	0.740	0.63
132_L	150_I	0.736	0.63
76_F	79_H	0.728	0.62
94_V	155_F	0.725	0.62
9_L	13_A	0.722	0.61
113_V	135_S	0.721	0.61
100_A	153_L	0.719	0.61
36_V	100_A	0.718	0.61
19_I	22_L	0.714	0.60
3_L	11_R	0.712	0.60
2_I	99_V	0.711	0.60
78_L	134_L	0.711	0.60
29_V	54_H	0.710	0.60
30_Q	106_S	0.710	0.60
38_L	86_G	0.709	0.60
109_G	172_S	0.708	0.60
42_F	86_G	0.701	0.59
110_R	128_G	0.700	0.59
32_A	136_N	0.698	0.59
68_T	72_D	0.697	0.59
36_V	150_I	0.697	0.59
77_I	153_L	0.692	0.58
38_L	144_L	0.691	0.58
66_T	69_V	0.691	0.58
37_R	90_E	0.686	0.57
111_L	115_V	0.677	0.56
99_V	121_F	0.673	0.56
29_V	167_G	0.668	0.55
12_L	20_E	0.668	0.55
181_Q	184_R	0.667	0.55
5_D	8_I	0.663	0.55
54_H	141_P	0.662	0.55
22_L	25_V	0.661	0.55
103_E	126_F	0.654	0.54
154_V	158_L	0.654	0.54
38_L	84_V	0.652	0.54
109_G	132_L	0.652	0.54
4_S	159_T	0.651	0.53
80_P	141_P	0.651	0.53
138_G	142_V	0.650	0.53
82_D	149_R	0.650	0.53
63_E	66_T	0.649	0.53
85_L	113_V	0.649	0.53
149_R	154_V	0.644	0.53
35_D	128_G	0.642	0.52
11_R	155_F	0.638	0.52
83_F	135_S	0.636	0.52
16_D	19_I	0.633	0.51
120_G	126_F	0.633	0.51
65_V	68_T	0.632	0.51
101_Q	154_V	0.629	0.51
100_A	126_F	0.627	0.51
42_F	146_P	0.627	0.51
54_H	143_A	0.623	0.50
30_Q	107_S	0.618	0.50
175_Q	179_G	0.614	0.49
46_E	78_L	0.612	0.49
116_H	133_E	0.611	0.49
171_G	176_D	0.610	0.49
88_T	130_V	0.608	0.49
72_D	75_E	0.602	0.48
88_T	104_G	0.601	0.48
100_A	124_P	0.599	0.48
116_H	121_F	0.599	0.48
32_A	162_A	0.589	0.47
76_F	84_V	0.588	0.46
167_G	178_D	0.586	0.46
136_N	142_V	0.582	0.46
129_R	178_D	0.582	0.46
46_E	60_E	0.581	0.46
92_V	153_L	0.580	0.45
35_D	155_F	0.579	0.45
102_V	115_V	0.576	0.45
125_G	158_L	0.572	0.45
99_V	137_L	0.571	0.44
141_P	151_S	0.569	0.44
96_R	155_F	0.568	0.44
32_A	145_T	0.567	0.44
18_A	91_R	0.567	0.44
106_S	128_G	0.566	0.44
60_E	179_G	0.566	0.44
33_S	109_G	0.566	0.44
109_G	120_G	0.565	0.44
134_L	144_L	0.564	0.44
105_R	173_K	0.564	0.44
107_S	149_R	0.563	0.44
2_I	50_V	0.562	0.43
104_G	116_H	0.561	0.43
32_A	121_F	0.557	0.43
167_G	175_Q	0.557	0.43
13_A	22_L	0.552	0.42
100_A	130_V	0.552	0.42
103_E	107_S	0.548	0.42
12_L	34_V	0.546	0.42
75_E	144_L	0.545	0.42
103_E	154_V	0.544	0.42
25_V	28_Q	0.541	0.41
31_P	104_G	0.539	0.41
33_S	121_F	0.537	0.41
99_V	154_V	0.534	0.40
9_L	178_D	0.532	0.40
68_T	146_P	0.532	0.40
144_L	158_L	0.529	0.40
6_Q	10_A	0.529	0.40
104_G	130_V	0.527	0.40
21_P	29_V	0.527	0.40
86_G	118_T	0.526	0.40
13_A	24_D	0.525	0.39
49_N	84_V	0.525	0.39
36_V	157_E	0.523	0.39
100_A	129_R	0.519	0.39
158_L	162_A	0.518	0.39
43_L	76_F	0.516	0.38
24_D	66_T	0.515	0.38
118_T	126_F	0.514	0.38
30_Q	109_G	0.512	0.38
59_D	160_S	0.512	0.38
24_D	36_V	0.512	0.38
20_E	23_E	0.511	0.38
57_R	60_E	0.509	0.38
128_G	152_Q	0.507	0.38
52_C	77_I	0.501	0.37
143_A	146_P	0.500	0.37

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	0.9538	100	0.202	Contact Map
2qxxA	3	0.9641	100	0.217	Contact Map
1pkhA	5	0.8359	100	0.225	Contact Map
4xjcA	3	0.9077	100	0.25	Contact Map
3km3A	4	0.759	100	0.287	Contact Map
4dhkA	5	0.8	100	0.289	Contact Map
2r9qA	4	0.8359	100	0.303	Contact Map
2yzjA	3	0.8103	100	0.336	Contact Map
3lqwA	3	0.6359	99.9	0.624	Contact Map
1f7dA	3	0.5846	99.9	0.642	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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