YBEY - BACSU - GREMLIN Contacts

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YBEY - Endoribonuclease YbeY

UniProt:	P46347	Sequences: MSLLIDIVDETGSVSEEMLKEVENLLQFAAEREGVQDQAEVSVTIVSNDDIHQINKEYRGKDAPTDVISFALEEEGEGEIEIVGAEMPPVLGDIIISADRTREQAEEYNHSFKRELGFLAVHGFLHLLGYDHMTKEEEEEMFTKQKELLDAYGLKRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	157 (133)
Sequences:	3746 (2648)
Seq/√Len:	229.6

ECOLI - YBEY
BACSU - YBEY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
52_H	62_D	3.167	1.00
48_N	97_S	3.134	1.00
48_N	103_E	2.558	1.00
142_F	145_Q	2.420	1.00
33_E	144_K	2.411	1.00
52_H	63_A	2.316	1.00
100_R	103_E	2.252	1.00
53_Q	57_E	2.246	1.00
48_N	100_R	2.159	1.00
56_K	62_D	2.149	1.00
52_H	56_K	2.089	1.00
45_I	98_A	2.069	1.00
48_N	99_D	1.943	1.00
66_D	104_Q	1.789	1.00
44_T	95_I	1.715	1.00
133_M	137_E	1.703	1.00
22_V	43_V	1.684	1.00
134_T	137_E	1.673	1.00
28_F	151_A	1.656	1.00
52_H	64_P	1.649	1.00
46_V	50_D	1.618	1.00
26_L	124_F	1.597	1.00
46_V	51_I	1.573	1.00
54_I	95_I	1.555	1.00
101_T	119_L	1.552	1.00
146_K	150_D	1.545	1.00
114_R	154_L	1.532	1.00
54_I	68_I	1.499	1.00
96_I	120_A	1.482	1.00
102_R	112_F	1.480	1.00
101_T	116_L	1.476	1.00
138_E	142_F	1.460	1.00
144_K	147_E	1.452	1.00
143_T	147_E	1.435	1.00
50_D	53_Q	1.434	1.00
46_V	95_I	1.414	1.00
66_D	115_E	1.409	1.00
51_I	64_P	1.408	1.00
32_R	147_E	1.403	1.00
96_I	101_T	1.399	1.00
32_R	151_A	1.377	1.00
104_Q	115_E	1.351	1.00
22_V	120_A	1.349	1.00
118_F	138_E	1.300	1.00
117_G	154_L	1.284	1.00
21_E	113_K	1.256	1.00
30_A	124_F	1.250	1.00
73_E	89_P	1.246	1.00
23_E	27_Q	1.240	1.00
97_S	100_R	1.224	1.00
118_F	145_Q	1.222	1.00
71_A	74_E	1.210	1.00
29_A	121_V	1.207	1.00
101_T	112_F	1.206	1.00
19_L	23_E	1.184	1.00
42_S	93_D	1.184	1.00
98_A	102_R	1.177	1.00
44_T	50_D	1.162	1.00
111_S	114_R	1.149	1.00
67_V	94_I	1.143	1.00
102_R	106_E	1.129	1.00
47_S	50_D	1.111	1.00
103_E	107_E	1.069	1.00
69_S	92_G	1.021	1.00
55_N	59_R	1.020	1.00
139_E	143_T	1.020	1.00
61_K	68_I	1.011	1.00
104_Q	110_H	1.007	1.00
140_E	144_K	0.986	1.00
26_L	120_A	0.973	1.00
72_L	90_V	0.959	1.00
21_E	24_N	0.955	1.00
130_Y	144_K	0.952	1.00
121_V	148_L	0.948	1.00
147_E	151_A	0.946	1.00
118_F	142_F	0.939	1.00
21_E	25_L	0.938	1.00
135_K	139_E	0.937	1.00
98_A	116_L	0.937	1.00
20_K	24_N	0.936	1.00
27_Q	31_E	0.930	1.00
64_P	97_S	0.924	1.00
55_N	61_K	0.922	1.00
41_V	124_F	0.901	0.99
25_L	117_G	0.897	0.99
28_F	152_Y	0.883	0.99
29_A	124_F	0.880	0.99
45_I	116_L	0.878	0.99
43_V	94_I	0.877	0.99
69_S	127_L	0.875	0.99
43_V	120_A	0.871	0.99
24_N	28_F	0.870	0.99
52_H	61_K	0.859	0.99
26_L	30_A	0.857	0.99
25_L	152_Y	0.856	0.99
110_H	115_E	0.847	0.99
75_E	78_G	0.842	0.99
28_F	32_R	0.840	0.99
71_A	75_E	0.840	0.99
64_P	100_R	0.837	0.99
48_N	64_P	0.837	0.99
130_Y	140_E	0.835	0.99
21_E	117_G	0.829	0.99
66_D	110_H	0.827	0.99
44_T	93_D	0.821	0.99
40_E	90_V	0.815	0.99
59_R	68_I	0.813	0.99
112_F	116_L	0.811	0.99
138_E	145_Q	0.807	0.99
47_S	99_D	0.806	0.99
59_R	63_A	0.803	0.99
115_E	118_F	0.798	0.99
32_R	148_L	0.793	0.99
91_L	128_L	0.788	0.99
71_A	123_G	0.782	0.98
71_A	93_D	0.780	0.98
67_V	123_G	0.779	0.98
92_G	127_L	0.775	0.98
102_R	105_A	0.771	0.98
114_R	153_G	0.759	0.98
69_S	91_L	0.755	0.98
124_F	128_L	0.753	0.98
135_K	138_E	0.748	0.98
51_I	97_S	0.746	0.98
54_I	58_Y	0.746	0.98
51_I	65_T	0.745	0.98
66_D	142_F	0.733	0.98
22_V	116_L	0.732	0.98
68_I	71_A	0.729	0.98
66_D	118_F	0.718	0.97
104_Q	118_F	0.718	0.97
33_E	148_L	0.713	0.97
33_E	130_Y	0.712	0.97
143_T	146_K	0.708	0.97
51_I	94_I	0.708	0.97
58_Y	70_F	0.707	0.97
118_F	146_K	0.705	0.97
28_F	31_E	0.702	0.97
67_V	119_L	0.698	0.97
51_I	63_A	0.696	0.97
26_L	43_V	0.694	0.97
55_N	62_D	0.690	0.97
110_H	118_F	0.688	0.97
46_V	97_S	0.682	0.96
120_A	124_F	0.677	0.96
114_R	118_F	0.672	0.96
51_I	95_I	0.656	0.96
39_A	89_P	0.655	0.96
18_M	21_E	0.646	0.95
33_E	128_L	0.643	0.95
66_D	146_K	0.642	0.95
146_K	149_L	0.642	0.95
121_V	149_L	0.640	0.95
125_L	148_L	0.633	0.95
72_L	91_L	0.627	0.94
144_K	148_L	0.625	0.94
51_I	100_R	0.624	0.94
94_I	123_G	0.623	0.94
106_E	112_F	0.620	0.94
125_L	141_M	0.615	0.94
121_V	125_L	0.608	0.93
67_V	101_T	0.607	0.93
53_Q	56_K	0.605	0.93
147_E	150_D	0.599	0.93
22_V	45_I	0.598	0.93
24_N	113_K	0.597	0.93
110_H	114_R	0.596	0.93
55_N	68_I	0.596	0.93
26_L	41_V	0.594	0.93
149_L	154_L	0.591	0.92
56_K	63_A	0.591	0.92
72_L	127_L	0.590	0.92
105_A	111_S	0.580	0.92
35_V	39_A	0.573	0.91
106_E	109_N	0.572	0.91
113_K	154_L	0.569	0.91
90_V	95_I	0.566	0.91
29_A	33_E	0.560	0.90
134_T	139_E	0.550	0.90
42_S	90_V	0.544	0.89
22_V	25_L	0.540	0.89
29_A	148_L	0.531	0.88
75_E	89_P	0.527	0.87
136_E	139_E	0.527	0.87
118_F	149_L	0.525	0.87
59_R	132_H	0.520	0.87
61_K	132_H	0.520	0.87
137_E	140_E	0.519	0.87
119_L	132_H	0.518	0.87
25_L	121_V	0.517	0.86
51_I	96_I	0.516	0.86
104_Q	119_L	0.514	0.86
13_S	16_E	0.513	0.86
71_A	133_M	0.510	0.86
71_A	91_L	0.508	0.85
25_L	120_A	0.507	0.85
28_F	148_L	0.505	0.85
54_I	94_I	0.504	0.85
139_E	142_F	0.500	0.85
63_A	100_R	0.500	0.85

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
1xm5A	1	0.9363	100	0.14	Contact Map
1xaxA	1	0.9045	100	0.14	Contact Map
1oz9A	1	0.8917	100	0.161	Contact Map
1tviA	1	0.8662	100	0.195	Contact Map
1lmlA	1	0.8535	67.2	0.913	Contact Map
1hv5A	2	0.8535	61.4	0.916	Contact Map
3ayuA	1	0.8471	56.7	0.918	Contact Map
4in9A	1	0.8471	51.8	0.921	Contact Map
1g9kA	3	0.8344	51	0.921	Contact Map
1k7iA	1	0.879	50.1	0.922	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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