DNAD - BACSU - GREMLIN Contacts

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DNAD - DNA replication protein DnaD

UniProt:	P39787	Sequences: MKKQQFIDMQEQGTSTIPNLLLTHYKQLGLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQPLWGKLYEYIQLAQNQTQERKAEGEQKSLYTIFEEEFARPLSPLECETLAIWQDQDQHDAQLIKHALKEAVLSGKLSFRYIDRILFEWKKNGLKTVEQAKIHSQKFRRVQAKQNEPQKEYKRQVPFYNWLEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	232 (200)
Sequences:	1257 (1046)
Seq/√Len:	73.9

BACSU - DNAD YQAL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_S	19_N	6.093	1.00
193_L	199_A	4.647	1.00
194_K	198_Q	4.364	1.00
23_T	43_M	4.356	1.00
191_N	202_H	3.682	1.00
193_L	202_H	3.247	1.00
133_F	167_L	3.108	1.00
139_R	145_E	3.020	1.00
169_E	203_S	2.948	1.00
166_A	185_L	2.925	1.00
148_T	182_D	2.742	1.00
30_L	75_F	2.666	1.00
193_L	198_Q	2.568	1.00
17_I	39_L	2.460	1.00
165_H	168_K	2.333	1.00
34_E	74_M	2.323	1.00
37_L	71_R	2.184	1.00
57_L	68_C	2.045	1.00
152_W	182_D	2.041	1.00
183_R	186_F	2.030	1.00
41_I	72_L	2.015	1.00
170_A	181_I	1.949	1.00
55_N	65_V	1.914	1.00
131_T	134_E	1.802	1.00
30_L	80_F	1.795	1.00
162_L	199_A	1.773	1.00
130_Y	141_L	1.762	1.00
145_E	178_F	1.737	1.00
162_L	193_L	1.733	1.00
162_L	196_V	1.727	1.00
199_A	203_S	1.658	1.00
132_I	164_K	1.650	1.00
117_T	120_R	1.647	1.00
134_E	141_L	1.593	0.99
179_R	182_D	1.584	0.99
165_H	169_E	1.576	0.99
151_I	155_Q	1.563	0.99
180_Y	184_I	1.539	0.99
129_L	167_L	1.536	0.99
31_N	34_E	1.530	0.99
201_I	204_Q	1.502	0.99
112_L	116_Q	1.492	0.99
24_H	27_Q	1.472	0.99
58_Q	64_S	1.468	0.99
170_A	184_I	1.420	0.99
99_L	102_L	1.379	0.98
33_T	67_E	1.340	0.98
57_L	60_G	1.324	0.98
32_E	35_L	1.319	0.98
44_H	52_P	1.316	0.98
67_E	70_N	1.310	0.98
153_Q	163_I	1.293	0.98
17_I	42_K	1.273	0.97
195_T	198_Q	1.273	0.97
169_E	184_I	1.269	0.97
166_A	170_A	1.250	0.97
158_H	189_K	1.239	0.97
34_E	71_R	1.238	0.97
167_L	181_I	1.236	0.97
130_Y	154_D	1.229	0.97
58_Q	65_V	1.211	0.96
29_G	78_K	1.195	0.96
152_W	184_I	1.191	0.96
182_D	186_F	1.189	0.96
37_L	41_I	1.184	0.96
133_F	136_E	1.177	0.96
54_P	72_L	1.171	0.96
94_F	97_Y	1.170	0.95
197_E	200_K	1.166	0.95
146_C	150_A	1.165	0.95
61_M	71_R	1.164	0.95
205_K	208_R	1.162	0.95
198_Q	201_I	1.152	0.95
58_Q	68_C	1.147	0.95
37_L	90_N	1.141	0.95
150_A	154_D	1.141	0.95
175_K	178_F	1.137	0.95
130_Y	150_A	1.125	0.94
132_I	136_E	1.124	0.94
98_S	103_W	1.114	0.94
35_L	63_I	1.114	0.94
187_E	191_N	1.110	0.94
115_N	118_Q	1.108	0.94
126_Q	160_A	1.102	0.94
15_S	43_M	1.100	0.94
73_R	77_Q	1.082	0.93
132_I	135_E	1.063	0.93
172_L	182_D	1.049	0.92
32_E	36_I	1.034	0.91
165_H	200_K	1.033	0.91
44_H	60_G	1.030	0.91
133_F	145_E	1.015	0.91
159_D	162_L	1.015	0.91
137_F	171_V	1.015	0.91
99_L	103_W	1.010	0.90
13_G	19_N	0.997	0.90
148_T	199_A	0.990	0.90
30_L	35_L	0.971	0.89
19_N	43_M	0.966	0.88
136_E	171_V	0.955	0.88
133_F	171_V	0.953	0.88
37_L	61_M	0.946	0.87
76_I	82_F	0.939	0.87
20_L	24_H	0.938	0.87
129_L	163_I	0.935	0.87
175_K	183_R	0.920	0.86
114_Q	118_Q	0.914	0.86
126_Q	150_A	0.907	0.85
200_K	204_Q	0.900	0.85
113_A	120_R	0.896	0.84
15_S	21_L	0.891	0.84
38_L	61_M	0.891	0.84
133_F	149_L	0.889	0.84
148_T	183_R	0.888	0.84
144_L	178_F	0.881	0.83
15_S	22_L	0.878	0.83
162_L	188_W	0.877	0.83
84_E	98_S	0.867	0.82
192_G	202_H	0.863	0.82
148_T	178_F	0.860	0.82
133_F	181_I	0.859	0.82
199_A	206_F	0.856	0.82
137_F	167_L	0.856	0.82
161_Q	199_A	0.853	0.81
141_L	178_F	0.852	0.81
104_G	108_E	0.851	0.81
32_E	62_S	0.849	0.81
196_V	200_K	0.846	0.81
10_Q	14_T	0.845	0.81
36_I	74_M	0.840	0.80
169_E	185_L	0.833	0.80
136_E	169_E	0.824	0.79
115_N	120_R	0.821	0.79
183_R	187_E	0.814	0.78
156_D	185_L	0.811	0.78
144_L	177_S	0.809	0.78
115_N	119_E	0.801	0.77
61_M	158_H	0.800	0.77
136_E	164_K	0.799	0.77
113_A	116_Q	0.797	0.77
74_M	78_K	0.796	0.77
142_S	179_R	0.789	0.76
143_P	147_E	0.787	0.76
54_P	69_T	0.783	0.75
134_E	138_A	0.779	0.75
38_L	80_F	0.777	0.75
170_A	185_L	0.776	0.75
34_E	78_K	0.775	0.75
203_S	206_F	0.771	0.74
37_L	57_L	0.767	0.74
152_W	163_I	0.765	0.74
96_K	100_Q	0.759	0.73
146_C	179_R	0.758	0.73
121_K	125_E	0.750	0.72
112_L	119_E	0.745	0.72
162_L	165_H	0.744	0.72
30_L	36_I	0.743	0.72
163_I	175_K	0.739	0.71
25_Y	32_E	0.739	0.71
55_N	59_E	0.736	0.71
204_Q	208_R	0.736	0.71
30_L	38_L	0.735	0.71
22_L	43_M	0.734	0.71
156_D	170_A	0.725	0.70
197_E	201_I	0.721	0.69
126_Q	163_I	0.720	0.69
165_H	203_S	0.719	0.69
166_A	169_E	0.714	0.69
36_I	40_K	0.713	0.68
172_L	179_R	0.711	0.68
134_E	146_C	0.710	0.68
148_T	165_H	0.701	0.67
95_E	98_S	0.699	0.67
69_T	90_N	0.698	0.67
49_S	56_Q	0.697	0.67
30_L	74_M	0.696	0.67
37_L	75_F	0.694	0.66
91_G	94_F	0.694	0.66
40_K	61_M	0.694	0.66
133_F	169_E	0.685	0.65
22_L	26_K	0.684	0.65
114_Q	117_T	0.683	0.65
130_Y	149_L	0.676	0.64
142_S	181_I	0.673	0.64
24_H	46_E	0.669	0.63
116_Q	119_E	0.668	0.63
137_F	145_E	0.668	0.63
92_I	95_E	0.667	0.63
112_L	118_Q	0.667	0.63
9_M	20_L	0.660	0.62
67_E	74_M	0.656	0.62
176_L	200_K	0.656	0.62
140_P	186_F	0.654	0.62
145_E	183_R	0.647	0.61
33_T	63_I	0.643	0.60
52_P	57_L	0.641	0.60
137_F	148_T	0.641	0.60
51_F	83_I	0.640	0.60
96_K	99_L	0.637	0.60
166_A	188_W	0.634	0.59
91_G	96_K	0.633	0.59
32_E	71_R	0.633	0.59
141_L	148_T	0.633	0.59
91_G	102_L	0.631	0.59
113_A	118_Q	0.630	0.59
119_E	127_K	0.627	0.59
26_K	38_L	0.625	0.58
73_R	192_G	0.624	0.58
81_L	89_Q	0.622	0.58
129_L	164_K	0.618	0.57
162_L	198_Q	0.617	0.57
158_H	163_I	0.617	0.57
136_E	168_K	0.616	0.57
191_N	205_K	0.615	0.57
12_Q	20_L	0.613	0.57
61_M	74_M	0.611	0.57
15_S	42_K	0.611	0.57
201_I	205_K	0.609	0.56
32_E	63_I	0.608	0.56
71_R	74_M	0.603	0.56
18_P	22_L	0.602	0.55
136_E	142_S	0.602	0.55
174_G	187_E	0.602	0.55
137_F	140_P	0.598	0.55
133_F	142_S	0.597	0.55
36_I	39_L	0.597	0.55
73_R	76_I	0.596	0.55
36_I	75_F	0.596	0.55
30_L	37_L	0.594	0.54
53_T	56_Q	0.594	0.54
203_S	207_R	0.589	0.54
133_F	137_F	0.588	0.54
173_S	203_S	0.586	0.53
129_L	133_F	0.585	0.53
31_N	54_P	0.579	0.53
34_E	62_S	0.579	0.53
34_E	37_L	0.579	0.53
10_Q	20_L	0.571	0.52
15_S	39_L	0.570	0.51
178_F	182_D	0.569	0.51
144_L	185_L	0.569	0.51
110_I	116_Q	0.567	0.51
167_L	171_V	0.565	0.51
149_L	152_W	0.563	0.51
136_E	172_L	0.563	0.51
128_S	152_W	0.563	0.51
141_L	145_E	0.563	0.51
101_P	106_L	0.562	0.50
135_E	191_N	0.559	0.50
16_T	19_N	0.559	0.50
48_G	72_L	0.557	0.50
175_K	184_I	0.556	0.50
141_L	160_A	0.554	0.49
26_K	36_I	0.554	0.49
64_S	67_E	0.553	0.49
114_Q	120_R	0.549	0.49
118_Q	123_E	0.548	0.49
134_E	188_W	0.548	0.49
144_L	147_E	0.547	0.49
13_G	16_T	0.544	0.48
25_Y	30_L	0.542	0.48
24_H	63_I	0.542	0.48
83_I	95_E	0.541	0.48
153_Q	158_H	0.540	0.48
159_D	194_K	0.538	0.47
128_S	177_S	0.538	0.47
57_L	61_M	0.537	0.47
164_K	177_S	0.536	0.47
138_A	178_F	0.533	0.47
41_I	81_L	0.533	0.47
17_I	114_Q	0.533	0.47
165_H	199_A	0.532	0.47
200_K	203_S	0.532	0.47
156_D	169_E	0.532	0.47
64_S	70_N	0.527	0.46
112_L	117_T	0.525	0.46
94_F	98_S	0.523	0.46
160_A	177_S	0.522	0.46
170_A	175_K	0.521	0.45
37_L	68_C	0.521	0.45
176_L	192_G	0.521	0.45
196_V	199_A	0.520	0.45
21_L	26_K	0.520	0.45
168_K	177_S	0.519	0.45
149_L	160_A	0.519	0.45
21_L	35_L	0.519	0.45
136_E	167_L	0.518	0.45
31_N	74_M	0.518	0.45
27_Q	68_C	0.517	0.45
48_G	58_Q	0.515	0.45
199_A	202_H	0.515	0.45
30_L	61_M	0.515	0.45
88_D	94_F	0.515	0.45
133_F	170_A	0.514	0.45
158_H	185_L	0.511	0.44
155_Q	189_K	0.507	0.44
129_L	149_L	0.506	0.44
18_P	75_F	0.503	0.43
35_L	39_L	0.500	0.43
180_Y	188_W	0.500	0.43

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
2zc2A	1	0.3233	99.8	0.601	Contact Map
2i5uA	1	0.3017	99.8	0.635	Contact Map
2v79A	4	0.5043	99.5	0.708	Contact Map
2vn2A	4	0.4741	99	0.769	Contact Map
4ptaD	3	0.4612	97.9	0.832	Contact Map
4pt7A	3	0.5086	97.8	0.836	Contact Map
3bjaA	2	0.5948	96.4	0.868	Contact Map
3broA	2	0.5991	96.4	0.869	Contact Map
3kp7A	2	0.5862	96.3	0.869	Contact Map
3jw4A	2	0.5431	96.2	0.87	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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