YFCE - ECOLI - GREMLIN Contacts

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YFCE - Phosphodiesterase YfcE

UniProt:	P67095	Sequences: MMKLMFASDIHGSLPATERVLELFAQSGAQWLVILGDVLNHGPRNALPEGYAPAKVAERLNEVAHKVIAVRGNCDSEVDQMLLHFPITAPWQQVLLEKQRLFLTHGHLFGPENLPALNQNDVLVYGHTHLPVAEQRGEIFHFNPGSVSIPKGGNPASYGMLDNDVLSVIALNDQSIIAQVAINP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14108
Length:	184 (154)
Sequences:	4208 (3313)
Seq/√Len:	266.9

ECOLI - YFCE
BACSU - YSNB
HALSA - Q9HMV3 Q9HMP6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_L	124_V	4.085	1.00
33_V	103_L	3.829	1.00
142_F	159_G	3.788	1.00
23_L	158_Y	2.861	1.00
31_W	68_I	2.846	1.00
5_M	24_F	2.792	1.00
133_A	140_F	2.704	1.00
101_L	122_V	2.537	1.00
5_M	29_A	2.504	1.00
35_L	103_L	2.323	1.00
18_E	59_R	2.322	1.00
125_Y	132_V	2.291	1.00
10_I	34_I	2.254	1.00
6_F	124_V	2.245	1.00
102_F	120_N	2.213	1.00
99_Q	121_D	2.169	1.00
6_F	161_L	2.058	1.00
10_I	147_V	1.967	1.00
3_K	162_D	1.949	1.00
100_R	121_D	1.806	1.00
125_Y	141_H	1.767	1.00
131_P	157_S	1.738	1.00
68_I	92_Q	1.722	1.00
21_L	59_R	1.700	1.00
29_A	160_M	1.646	1.00
38_V	69_A	1.596	1.00
6_F	142_F	1.583	1.00
7_A	20_V	1.581	1.00
44_R	55_K	1.511	1.00
5_M	20_V	1.506	1.00
8_S	35_L	1.473	1.00
14_L	55_K	1.434	1.00
34_I	69_A	1.425	1.00
10_I	17_T	1.419	1.00
34_I	38_V	1.416	1.00
8_S	126_G	1.394	1.00
152_G	157_S	1.381	1.00
18_E	22_E	1.377	1.00
128_T	143_N	1.377	1.00
32_L	67_V	1.374	1.00
3_K	160_M	1.370	1.00
13_S	16_A	1.367	1.00
7_A	17_T	1.345	1.00
14_L	59_R	1.344	1.00
24_F	32_L	1.335	1.00
20_V	147_V	1.332	1.00
16_A	156_A	1.331	1.00
150_P	156_A	1.298	1.00
54_A	58_E	1.292	1.00
135_Q	140_F	1.292	1.00
144_P	159_G	1.287	1.00
19_R	23_L	1.284	1.00
13_S	148_S	1.256	1.00
5_M	158_Y	1.254	1.00
59_R	62_E	1.226	1.00
5_M	32_L	1.225	1.00
113_N	117_L	1.222	1.00
104_T	109_F	1.216	1.00
135_Q	138_E	1.199	1.00
14_L	18_E	1.159	1.00
152_G	172_N	1.137	1.00
147_V	158_Y	1.133	1.00
103_L	124_V	1.126	1.00
133_A	142_F	1.103	1.00
15_P	18_E	1.092	1.00
4_L	31_W	1.088	1.00
114_L	118_N	1.063	1.00
99_Q	166_L	1.046	1.00
25_A	65_H	1.042	1.00
39_L	74_C	1.021	1.00
76_S	111_P	1.020	1.00
7_A	34_I	1.019	1.00
104_T	108_L	1.013	1.00
122_V	140_F	1.009	1.00
86_P	89_A	0.992	1.00
23_L	171_L	0.984	1.00
95_L	100_R	0.982	1.00
124_V	142_F	0.981	1.00
146_S	150_P	0.974	1.00
15_P	44_R	0.966	1.00
33_V	94_V	0.957	1.00
112_E	116_A	0.956	1.00
24_F	158_Y	0.949	1.00
24_F	29_A	0.945	1.00
20_V	24_F	0.936	1.00
123_L	139_I	0.917	1.00
122_V	161_L	0.911	1.00
5_M	160_M	0.907	1.00
38_V	56_V	0.907	1.00
20_V	158_Y	0.905	1.00
25_A	63_V	0.898	1.00
164_D	167_S	0.894	1.00
106_G	128_T	0.892	1.00
99_Q	163_N	0.890	1.00
25_A	28_G	0.887	1.00
85_F	89_A	0.885	1.00
97_E	163_N	0.871	1.00
7_A	10_I	0.862	1.00
89_A	92_Q	0.861	1.00
57_A	61_N	0.861	1.00
71_R	76_S	0.855	1.00
7_A	32_L	0.852	1.00
63_V	66_K	0.848	1.00
4_L	161_L	0.844	1.00
146_S	151_K	0.840	0.99
73_N	127_H	0.839	0.99
6_F	33_V	0.829	0.99
19_R	22_E	0.827	0.99
53_P	57_A	0.827	0.99
31_W	96_L	0.824	0.99
124_V	161_L	0.824	0.99
2_M	162_D	0.820	0.99
115_P	139_I	0.810	0.99
120_N	123_L	0.810	0.99
16_A	19_R	0.808	0.99
136_R	139_I	0.805	0.99
125_Y	128_T	0.795	0.99
99_Q	122_V	0.793	0.99
24_F	28_G	0.793	0.99
2_M	96_L	0.782	0.99
22_E	25_A	0.779	0.99
87_I	90_P	0.772	0.99
131_P	154_N	0.766	0.99
111_P	125_Y	0.762	0.99
2_M	30_Q	0.761	0.99
54_A	57_A	0.760	0.99
89_A	95_L	0.758	0.99
74_C	149_I	0.757	0.99
21_L	63_V	0.756	0.99
159_G	170_A	0.747	0.99
115_P	123_L	0.746	0.99
123_L	141_H	0.744	0.99
104_T	123_L	0.743	0.99
162_D	169_I	0.742	0.99
90_P	107_H	0.735	0.99
58_E	61_N	0.729	0.99
74_C	151_K	0.723	0.98
107_H	110_G	0.722	0.98
107_H	158_Y	0.716	0.98
82_L	86_P	0.715	0.98
82_L	85_F	0.713	0.98
29_A	32_L	0.708	0.98
18_E	55_K	0.706	0.98
163_N	166_L	0.699	0.98
133_A	170_A	0.697	0.98
157_S	172_N	0.681	0.98
117_L	120_N	0.681	0.98
35_L	70_V	0.680	0.98
116_A	137_G	0.680	0.98
124_V	144_P	0.670	0.98
101_L	124_V	0.657	0.97
83_L	86_P	0.656	0.97
95_L	98_K	0.653	0.97
9_D	129_H	0.651	0.97
16_A	148_S	0.649	0.97
17_T	60_L	0.649	0.97
31_W	66_K	0.645	0.97
15_P	19_R	0.640	0.97
11_H	129_H	0.639	0.97
44_R	56_V	0.634	0.97
106_G	110_G	0.633	0.97
112_E	136_R	0.631	0.96
34_I	75_D	0.627	0.96
55_K	58_E	0.627	0.96
5_M	28_G	0.627	0.96
126_G	144_P	0.626	0.96
21_L	25_A	0.624	0.96
101_L	163_N	0.622	0.96
92_Q	103_L	0.616	0.96
60_L	67_V	0.612	0.96
81_M	86_P	0.607	0.96
91_W	94_V	0.606	0.96
7_A	24_F	0.604	0.95
96_L	99_Q	0.600	0.95
119_Q	167_S	0.599	0.95
97_E	166_L	0.598	0.95
17_T	20_V	0.592	0.95
76_S	80_Q	0.592	0.95
17_T	56_V	0.591	0.95
154_N	172_N	0.590	0.95
128_T	145_G	0.588	0.95
131_P	152_G	0.587	0.95
17_T	147_V	0.577	0.94
102_F	118_N	0.577	0.94
59_R	63_V	0.576	0.94
54_A	61_N	0.576	0.94
12_G	53_P	0.572	0.94
5_M	23_L	0.572	0.94
120_N	139_I	0.569	0.94
7_A	147_V	0.563	0.93
38_V	71_R	0.559	0.93
9_D	73_N	0.559	0.93
12_G	56_V	0.557	0.93
136_R	140_F	0.553	0.93
8_S	106_G	0.553	0.93
154_N	157_S	0.553	0.93
104_T	107_H	0.552	0.93
16_A	20_V	0.551	0.93
2_M	97_E	0.550	0.93
116_A	136_R	0.550	0.93
38_V	76_S	0.548	0.93
17_T	21_L	0.548	0.93
149_I	154_N	0.547	0.92
53_P	56_V	0.545	0.92
87_I	91_W	0.545	0.92
100_R	119_Q	0.544	0.92
20_V	23_L	0.540	0.92
2_M	164_D	0.538	0.92
93_Q	120_N	0.537	0.92
58_E	62_E	0.536	0.92
114_L	136_R	0.536	0.92
102_F	114_L	0.533	0.91
115_P	118_N	0.531	0.91
19_R	156_A	0.530	0.91
135_Q	168_V	0.530	0.91
10_I	38_V	0.528	0.91
3_K	30_Q	0.521	0.91
4_L	124_V	0.516	0.90
69_A	92_Q	0.514	0.90
91_W	114_L	0.513	0.90
106_G	150_P	0.513	0.90
159_G	168_V	0.511	0.90
33_V	101_L	0.510	0.90
22_E	138_E	0.509	0.90
2_M	163_N	0.508	0.89
14_L	44_R	0.508	0.89
98_K	121_D	0.507	0.89
55_K	59_R	0.507	0.89
88_T	95_L	0.505	0.89
85_F	95_L	0.500	0.89
112_E	139_I	0.500	0.89

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
1nnwA	2	0.9511	100	0.353	Contact Map
3qfmA	2	0.9457	100	0.377	Contact Map
1su1A	3	0.9837	100	0.385	Contact Map
3rqzA	1	0.9402	100	0.389	Contact Map
1s3lA	1	0.8533	100	0.445	Contact Map
3ck2A	1	0.8587	100	0.461	Contact Map
2a22A	1	0.9293	100	0.468	Contact Map
1uf3A	6	0.8641	100	0.48	Contact Map
1z2wA	2	0.8804	100	0.48	Contact Map
1g5bA	4	0.8261	100	0.488	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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