YMDB - ECOLI - GREMLIN Contacts

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YMDB - O-acetyl-ADP-ribose deacetylase

UniProt:	P0A8D6	Sequences: MKTRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQQGDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13874
Length:	177 (162)
Sequences:	3928 (2816)
Seq/√Len:	221.3

ECOLI - YMDB
SULSO - Y2899

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
141_V	156_F	3.026	1.00
6_H	153_Q	2.948	1.00
49_A	71_G	2.557	1.00
15_L	155_Y	2.464	1.00
94_D	132_A	2.423	1.00
160_D	163_N	2.401	1.00
114_T	152_E	2.395	1.00
49_A	69_L	2.294	1.00
42_A	46_L	2.169	1.00
67_I	111_N	2.096	1.00
67_I	107_L	2.092	1.00
99_D	103_N	2.031	1.00
45_A	72_D	2.014	1.00
64_H	103_N	1.963	1.00
89_G	93_E	1.937	1.00
164_A	168_E	1.935	1.00
62_T	96_L	1.894	1.00
103_N	106_R	1.884	1.00
102_L	140_T	1.851	1.00
9_Q	161_E	1.834	1.00
14_K	41_A	1.789	1.00
130_R	163_N	1.781	1.00
30_G	35_D	1.698	1.00
9_Q	164_A	1.662	1.00
77_A	113_Y	1.644	1.00
109_A	144_F	1.634	1.00
140_T	143_E	1.619	1.00
47_L	51_L	1.601	1.00
128_Y	132_A	1.576	1.00
105_L	144_F	1.563	1.00
130_R	166_L	1.544	1.00
128_Y	136_I	1.515	1.00
81_T	104_S	1.482	1.00
19_V	113_Y	1.469	1.00
42_A	71_G	1.464	1.00
107_L	110_A	1.440	1.00
161_E	165_H	1.438	1.00
98_Q	140_T	1.415	1.00
17_V	117_A	1.412	1.00
8_V	15_L	1.400	1.00
141_V	154_V	1.399	1.00
65_A	79_V	1.378	1.00
120_A	123_T	1.337	1.00
7_V	164_A	1.328	1.00
120_A	167_Y	1.321	1.00
144_F	148_H	1.301	1.00
53_V	66_V	1.298	1.00
86_W	93_E	1.289	1.00
45_A	71_G	1.265	1.00
106_R	144_F	1.265	1.00
20_I	38_I	1.259	1.00
130_R	162_E	1.249	1.00
166_L	170_L	1.245	1.00
70_A	75_A	1.240	1.00
60_C	66_V	1.221	1.00
81_T	100_A	1.216	1.00
109_A	151_P	1.209	1.00
158_C	164_A	1.205	1.00
15_L	157_V	1.198	1.00
68_T	80_H	1.198	1.00
158_C	167_Y	1.195	1.00
61_P	66_V	1.188	1.00
94_D	128_Y	1.188	1.00
18_D	76_K	1.185	1.00
86_W	89_G	1.180	1.00
46_L	71_G	1.172	1.00
104_S	118_F	1.172	1.00
120_A	163_N	1.167	1.00
107_L	111_N	1.164	1.00
130_R	160_D	1.155	1.00
134_A	166_L	1.152	1.00
98_Q	139_K	1.151	1.00
83_G	122_S	1.148	1.00
131_A	169_R	1.143	1.00
77_A	111_N	1.133	1.00
109_A	148_H	1.128	1.00
101_Y	137_A	1.108	1.00
123_T	163_N	1.107	1.00
108_V	116_V	1.106	1.00
18_D	113_Y	1.105	1.00
79_V	104_S	1.057	1.00
19_V	79_V	1.046	1.00
35_D	39_H	1.029	1.00
48_D	52_K	1.025	1.00
120_A	134_A	1.024	1.00
106_R	110_A	1.016	1.00
98_Q	102_L	1.015	1.00
65_A	103_N	1.011	1.00
45_A	69_L	1.000	1.00
120_A	130_R	0.987	1.00
88_G	93_E	0.982	1.00
10_G	15_L	0.979	1.00
67_I	113_Y	0.975	1.00
36_G	40_R	0.975	1.00
139_K	143_E	0.967	1.00
10_G	157_V	0.962	1.00
10_G	14_K	0.953	1.00
163_N	167_Y	0.946	1.00
104_S	116_V	0.943	1.00
62_T	85_V	0.941	1.00
165_H	169_R	0.933	1.00
61_P	64_H	0.929	1.00
135_E	170_L	0.920	0.99
7_V	171_L	0.904	0.99
98_Q	143_E	0.904	0.99
26_P	82_V	0.900	0.99
45_A	48_D	0.896	0.99
138_V	171_L	0.896	0.99
29_M	51_L	0.890	0.99
88_G	91_Q	0.890	0.99
17_V	155_Y	0.884	0.99
142_S	146_T	0.883	0.99
69_L	77_A	0.879	0.99
87_R	91_Q	0.869	0.99
26_P	61_P	0.866	0.99
37_A	41_A	0.865	0.99
92_N	95_Q	0.864	0.99
29_M	47_L	0.858	0.99
16_A	74_P	0.853	0.99
86_W	132_A	0.846	0.99
123_T	133_A	0.845	0.99
102_L	106_R	0.841	0.99
98_Q	136_I	0.841	0.99
89_G	92_N	0.840	0.99
7_V	158_C	0.835	0.99
132_A	135_E	0.832	0.99
65_A	107_L	0.826	0.99
130_R	134_A	0.825	0.99
35_D	47_L	0.824	0.99
102_L	143_E	0.824	0.99
46_L	78_V	0.823	0.99
64_H	99_D	0.820	0.99
49_A	52_K	0.820	0.99
109_A	152_E	0.818	0.99
7_V	138_V	0.814	0.99
138_V	170_L	0.810	0.99
115_S	153_Q	0.809	0.99
136_I	140_T	0.798	0.99
95_Q	99_D	0.795	0.98
123_T	134_A	0.789	0.98
165_H	168_E	0.787	0.98
109_A	149_A	0.786	0.98
23_A	34_V	0.784	0.98
49_A	68_T	0.779	0.98
11_D	14_K	0.776	0.98
73_L	78_V	0.775	0.98
86_W	128_Y	0.774	0.98
151_P	154_V	0.769	0.98
108_V	113_Y	0.769	0.98
86_W	129_P	0.766	0.98
84_P	97_L	0.762	0.98
30_G	50_C	0.753	0.98
134_A	170_L	0.751	0.98
26_P	62_T	0.745	0.98
31_G	36_G	0.742	0.98
87_R	93_E	0.740	0.98
83_G	121_I	0.738	0.98
101_Y	133_A	0.735	0.97
93_E	96_L	0.728	0.97
131_A	166_L	0.727	0.97
109_A	150_L	0.725	0.97
163_N	166_L	0.711	0.97
94_D	98_Q	0.710	0.97
19_V	116_V	0.709	0.97
123_T	167_Y	0.705	0.97
94_D	136_I	0.702	0.97
120_A	158_C	0.698	0.97
92_N	96_L	0.698	0.97
26_P	59_D	0.697	0.97
134_A	167_Y	0.690	0.96
48_D	51_L	0.690	0.96
9_Q	160_D	0.690	0.96
112_S	150_L	0.681	0.96
46_L	69_L	0.674	0.96
30_G	39_H	0.673	0.96
58_G	66_V	0.670	0.96
30_G	47_L	0.667	0.96
120_A	166_L	0.666	0.95
33_G	36_G	0.662	0.95
44_P	48_D	0.660	0.95
135_E	139_K	0.656	0.95
167_Y	170_L	0.654	0.95
27_S	59_D	0.654	0.95
20_I	74_P	0.651	0.95
105_L	154_V	0.647	0.95
137_A	156_F	0.644	0.95
6_H	155_Y	0.644	0.95
24_A	31_G	0.644	0.95
50_C	53_V	0.641	0.94
65_A	81_T	0.631	0.94
133_A	137_A	0.627	0.94
20_I	73_L	0.626	0.94
120_A	156_F	0.622	0.94
156_F	167_Y	0.620	0.93
7_V	168_E	0.617	0.93
105_L	141_V	0.612	0.93
144_F	154_V	0.610	0.93
131_A	135_E	0.609	0.93
15_L	117_A	0.609	0.93
117_A	157_V	0.608	0.93
28_L	50_C	0.606	0.93
22_N	80_H	0.602	0.92
161_E	164_A	0.600	0.92
17_V	115_S	0.593	0.92
39_H	50_C	0.593	0.92
52_K	71_G	0.592	0.92
12_I	34_V	0.591	0.92
114_T	151_P	0.590	0.92
81_T	121_I	0.585	0.91
22_N	38_I	0.580	0.91
63_G	81_T	0.579	0.91
145_I	154_V	0.577	0.91
122_S	126_Y	0.566	0.90
113_Y	116_V	0.566	0.90
8_V	155_Y	0.559	0.89
123_T	130_R	0.559	0.89
13_T	38_I	0.555	0.89
42_A	69_L	0.555	0.89
128_Y	133_A	0.549	0.89
24_A	50_C	0.548	0.88
106_R	109_A	0.547	0.88
21_V	118_F	0.544	0.88
85_V	88_G	0.542	0.88
24_A	126_Y	0.539	0.88
24_A	33_G	0.537	0.87
28_L	53_V	0.537	0.87
140_T	144_F	0.533	0.87
120_A	160_D	0.532	0.87
87_R	92_N	0.528	0.87
60_C	82_V	0.527	0.86
107_L	113_Y	0.527	0.86
83_G	126_Y	0.524	0.86
39_H	46_L	0.524	0.86
117_A	155_Y	0.524	0.86
76_K	115_S	0.519	0.86
39_H	47_L	0.516	0.85
59_D	66_V	0.514	0.85
88_G	92_N	0.513	0.85
106_R	147_R	0.510	0.85
31_G	34_V	0.507	0.84
26_P	60_C	0.506	0.84
118_F	137_A	0.505	0.84
104_S	108_V	0.500	0.83

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
1spvA	1	0.9718	100	0.117	Contact Map
1yd9A	1	0.9887	100	0.135	Contact Map
2xd7A	1	0.9718	100	0.137	Contact Map
3q71A	1	0.9887	100	0.139	Contact Map
3q6zA	1	0.9887	100	0.143	Contact Map
4umlA	1	0.9718	100	0.143	Contact Map
2x47A	1	0.9774	100	0.144	Contact Map
4d86A	1	0.9887	100	0.147	Contact Map
4iqyA	1	0.9718	100	0.156	Contact Map
1vhuA	1	0.9774	100	0.18	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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