YGGS - ECOLI - GREMLIN Contacts

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YGGS - UPF0001 protein YggS

UniProt:	P67080	Sequences: MNDIAHNLAQVRDKISAAATRCGRSPEEITLLAVSKTKPASAIAEAIDAGQRQFGENYVQEGVDKIRHFQELGVTGLEWHFIGPLQSNKSRLVAEHFDWCHTIDRLRIATRLNDQRPAELPPLNVLIQINISDENSKSGIQLAELDELAAAVAELPRLRLRGLMAIPAPESEYVRQFEVARQMAVAFAGLKTRYPHIDTLSLGMSDDMEAAIAAGSTMVRIGTAIFGARDYSKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12979
Length:	234 (222)
Sequences:	4727 (3392)
Seq/√Len:	227.7

ECOLI - YGGS
BACSU - YLME

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_Q	78_E	3.734	1.00
124_N	159_R	3.549	1.00
14_K	209_E	2.975	1.00
113_N	157_R	2.927	1.00
177_F	180_A	2.834	1.00
38_K	42_A	2.719	1.00
87_S	107_R	2.679	1.00
84_P	138_S	2.670	1.00
140_I	148_L	2.478	1.00
19_A	29_I	2.370	1.00
124_N	161_R	2.344	1.00
44_A	48_D	2.324	1.00
62_G	97_F	2.225	1.00
21_R	213_A	2.166	1.00
106_L	151_A	2.148	1.00
110_T	151_A	2.147	1.00
199_T	217_T	1.998	1.00
34_V	82_I	1.995	1.00
32_L	218_M	1.982	1.00
15_I	31_L	1.976	1.00
111_R	115_Q	1.936	1.00
111_R	114_D	1.933	1.00
14_K	208_M	1.863	1.00
103_I	112_L	1.773	1.00
47_I	52_R	1.759	1.00
163_L	200_L	1.744	1.00
181_R	214_A	1.744	1.00
15_I	212_I	1.733	1.00
47_I	77_L	1.727	1.00
52_R	76_G	1.712	1.00
115_Q	118_A	1.711	1.00
30_T	53_Q	1.706	1.00
12_R	26_P	1.698	1.00
19_A	27_E	1.697	1.00
30_T	199_T	1.686	1.00
39_P	42_A	1.685	1.00
106_L	110_T	1.681	1.00
184_A	188_A	1.659	1.00
221_I	224_A	1.643	1.00
35_S	54_F	1.640	1.00
13_D	17_A	1.626	1.00
161_R	198_D	1.619	1.00
113_N	156_P	1.616	1.00
99_W	126_L	1.614	1.00
177_F	214_A	1.606	1.00
205_S	224_A	1.603	1.00
101_H	218_M	1.578	1.00
117_P	157_R	1.573	1.00
122_P	159_R	1.556	1.00
113_N	155_L	1.500	1.00
116_R	123_L	1.494	1.00
181_R	185_V	1.470	1.00
109_A	155_L	1.456	1.00
25_S	28_E	1.455	1.00
85_L	93_V	1.436	1.00
126_L	199_T	1.434	1.00
177_F	186_A	1.420	1.00
33_A	51_Q	1.418	1.00
127_I	148_L	1.383	1.00
103_I	125_V	1.375	1.00
151_A	154_E	1.362	1.00
127_I	149_A	1.358	1.00
59_V	81_F	1.346	1.00
78_E	98_D	1.327	1.00
144_E	147_E	1.318	1.00
133_D	141_Q	1.304	1.00
147_E	150_A	1.291	1.00
109_A	152_V	1.275	1.00
199_T	218_M	1.274	1.00
129_I	145_L	1.267	1.00
180_A	186_A	1.267	1.00
47_I	54_F	1.249	1.00
8_L	12_R	1.248	1.00
64_D	68_H	1.244	1.00
90_S	108_I	1.238	1.00
17_A	20_T	1.237	1.00
177_F	187_F	1.228	1.00
149_A	160_L	1.217	1.00
133_D	143_A	1.213	1.00
42_A	45_E	1.205	1.00
11_V	221_I	1.203	1.00
113_N	117_P	1.202	1.00
32_L	53_Q	1.194	1.00
44_A	69_F	1.180	1.00
40_A	68_H	1.179	1.00
16_S	20_T	1.175	1.00
94_A	123_L	1.152	1.00
66_I	96_H	1.144	1.00
87_S	105_R	1.127	1.00
21_R	209_E	1.127	1.00
19_A	25_S	1.125	1.00
46_A	49_A	1.119	1.00
60_Q	88_N	1.113	1.00
33_A	225_I	1.112	1.00
105_R	108_I	1.104	1.00
47_I	76_G	1.082	1.00
9_A	13_D	1.079	1.00
95_E	119_E	1.078	1.00
181_R	184_A	1.072	1.00
81_F	93_V	1.069	1.00
29_I	212_I	1.066	1.00
66_I	97_F	1.066	1.00
59_V	85_L	1.065	1.00
180_A	187_F	1.061	1.00
63_V	92_L	1.047	1.00
206_D	223_T	1.042	1.00
176_Q	179_V	1.040	1.00
172_E	175_R	1.038	1.00
59_V	63_V	1.033	1.00
173_Y	210_A	1.033	1.00
32_L	101_H	1.031	1.00
5_A	9_A	1.029	1.00
140_I	145_L	1.024	1.00
8_L	51_Q	1.022	1.00
93_V	97_F	1.022	1.00
179_V	182_Q	1.007	1.00
62_G	66_I	1.005	1.00
126_L	218_M	1.001	1.00
141_Q	144_E	1.000	1.00
19_A	26_P	0.997	1.00
98_D	124_N	0.996	1.00
46_A	225_I	0.994	1.00
110_T	155_L	0.991	1.00
126_L	161_R	0.989	1.00
110_T	114_D	0.987	1.00
43_I	54_F	0.984	1.00
178_E	214_A	0.972	1.00
146_D	150_A	0.964	1.00
127_I	140_I	0.960	1.00
12_R	16_S	0.951	1.00
30_T	218_M	0.944	1.00
87_S	111_R	0.942	1.00
131_I	176_Q	0.941	1.00
87_S	108_I	0.937	1.00
29_I	219_V	0.936	1.00
40_A	69_F	0.930	1.00
84_P	104_D	0.925	1.00
100_C	112_L	0.925	1.00
178_E	182_Q	0.919	1.00
180_A	184_A	0.918	1.00
19_A	28_E	0.910	0.99
210_A	214_A	0.910	0.99
63_V	96_H	0.909	0.99
18_A	22_C	0.908	0.99
37_T	57_N	0.906	0.99
37_T	58_Y	0.905	0.99
100_C	103_I	0.904	0.99
130_N	133_D	0.904	0.99
44_A	75_T	0.901	0.99
13_D	16_S	0.901	0.99
109_A	158_L	0.901	0.99
95_E	121_P	0.894	0.99
16_S	19_A	0.885	0.99
24_R	28_E	0.878	0.99
17_A	21_R	0.874	0.99
210_A	213_A	0.874	0.99
10_Q	14_K	0.873	0.99
19_A	24_R	0.873	0.99
8_L	46_A	0.865	0.99
194_Y	197_I	0.862	0.99
99_W	218_M	0.859	0.99
38_K	228_A	0.854	0.99
99_W	124_N	0.847	0.99
187_F	191_K	0.845	0.99
152_V	160_L	0.842	0.99
176_Q	180_A	0.836	0.99
142_L	186_A	0.836	0.99
59_V	93_V	0.834	0.99
90_S	111_R	0.830	0.99
58_Y	102_T	0.826	0.99
177_F	213_A	0.823	0.99
90_S	112_L	0.822	0.99
67_R	96_H	0.817	0.99
104_D	108_I	0.811	0.99
103_I	148_L	0.807	0.99
30_T	78_E	0.807	0.99
40_A	43_I	0.799	0.99
99_W	161_R	0.791	0.99
131_I	165_A	0.791	0.99
132_S	168_A	0.789	0.99
134_E	137_K	0.789	0.99
110_T	154_E	0.784	0.98
91_R	115_Q	0.783	0.98
69_F	77_L	0.782	0.98
125_V	158_L	0.782	0.98
31_L	221_I	0.775	0.98
90_S	94_A	0.772	0.98
131_I	180_A	0.767	0.98
80_H	99_W	0.765	0.98
81_F	85_L	0.763	0.98
35_S	226_F	0.762	0.98
103_I	108_I	0.761	0.98
114_D	118_A	0.759	0.98
128_Q	166_I	0.756	0.98
59_V	92_L	0.755	0.98
70_Q	76_G	0.754	0.98
176_Q	210_A	0.750	0.98
179_V	183_M	0.750	0.98
208_M	212_I	0.747	0.98
93_V	96_H	0.747	0.98
145_L	163_L	0.746	0.98
212_I	219_V	0.746	0.98
32_L	216_S	0.742	0.98
187_F	197_I	0.737	0.98
84_P	105_R	0.737	0.98
175_R	179_V	0.735	0.98
35_S	51_Q	0.721	0.97
185_V	189_G	0.719	0.97
16_S	26_P	0.714	0.97
165_A	180_A	0.713	0.97
24_R	27_E	0.712	0.97
159_R	196_H	0.711	0.97
100_C	123_L	0.708	0.97
115_Q	119_E	0.708	0.97
85_L	108_I	0.707	0.97
43_I	69_F	0.705	0.97
20_T	26_P	0.704	0.97
116_R	121_P	0.704	0.97
185_V	188_A	0.698	0.97
70_Q	75_T	0.690	0.97
53_Q	101_H	0.686	0.96
106_L	155_L	0.683	0.96
47_I	75_T	0.682	0.96
161_R	199_T	0.676	0.96
6_H	9_A	0.675	0.96
45_E	48_D	0.675	0.96
46_A	226_F	0.674	0.96
37_T	61_E	0.669	0.96
147_E	151_A	0.669	0.96
182_Q	186_A	0.664	0.96
15_I	29_I	0.661	0.96
175_R	178_E	0.660	0.96
37_T	230_D	0.657	0.96
90_S	115_Q	0.656	0.95
46_A	51_Q	0.655	0.95
151_A	155_L	0.653	0.95
55_G	82_I	0.652	0.95
44_A	70_Q	0.651	0.95
59_V	62_G	0.650	0.95
47_I	69_F	0.650	0.95
51_Q	54_F	0.646	0.95
138_S	166_I	0.646	0.95
94_A	121_P	0.641	0.95
117_P	156_P	0.639	0.95
99_W	199_T	0.637	0.95
163_L	183_M	0.636	0.95
44_A	68_H	0.635	0.95
186_A	190_L	0.633	0.95
62_G	93_V	0.633	0.95
116_R	122_P	0.631	0.94
120_L	157_R	0.629	0.94
132_S	167_P	0.628	0.94
149_A	197_I	0.625	0.94
95_E	123_L	0.625	0.94
7_N	10_Q	0.624	0.94
165_A	202_L	0.620	0.94
54_F	77_L	0.617	0.94
103_I	109_A	0.617	0.94
9_A	12_R	0.615	0.94
26_P	29_I	0.615	0.94
174_V	178_E	0.614	0.94
56_E	65_K	0.613	0.94
40_A	65_K	0.612	0.93
35_S	65_K	0.607	0.93
10_Q	13_D	0.605	0.93
40_A	44_A	0.605	0.93
61_E	229_R	0.600	0.93
184_A	187_F	0.598	0.93
150_A	153_A	0.596	0.93
177_F	184_A	0.595	0.93
186_A	189_G	0.592	0.92
66_I	70_Q	0.591	0.92
142_L	179_V	0.591	0.92
179_V	186_A	0.590	0.92
59_V	97_F	0.589	0.92
41_S	44_A	0.587	0.92
85_L	100_C	0.584	0.92
80_H	101_H	0.580	0.92
61_E	65_K	0.580	0.92
14_K	224_A	0.580	0.92
107_R	110_T	0.578	0.91
132_S	165_A	0.575	0.91
150_A	193_R	0.574	0.91
146_D	190_L	0.573	0.91
112_L	158_L	0.570	0.91
5_A	46_A	0.569	0.91
58_Y	166_I	0.566	0.91
8_L	225_I	0.565	0.90
166_I	204_M	0.560	0.90
169_P	206_D	0.557	0.90
11_V	208_M	0.554	0.90
142_L	146_D	0.553	0.90
92_L	95_E	0.553	0.90
66_I	79_W	0.551	0.89
127_I	145_L	0.549	0.89
33_A	226_F	0.548	0.89
37_T	43_I	0.546	0.89
18_A	209_E	0.545	0.89
41_S	68_H	0.544	0.89
133_D	142_L	0.541	0.89
146_D	149_A	0.541	0.89
11_V	18_A	0.534	0.88
187_F	190_L	0.530	0.88
170_E	175_R	0.530	0.88
183_M	187_F	0.528	0.87
190_L	193_R	0.527	0.87
140_I	144_E	0.525	0.87
5_A	49_A	0.524	0.87
18_A	212_I	0.522	0.87
149_A	190_L	0.521	0.87
182_Q	185_V	0.521	0.87
177_F	185_V	0.520	0.87
106_L	148_L	0.520	0.87
129_I	183_M	0.519	0.86
22_C	25_S	0.519	0.86
208_M	224_A	0.517	0.86
24_R	29_I	0.515	0.86
131_I	142_L	0.514	0.86
148_L	155_L	0.512	0.86
14_K	18_A	0.511	0.86
38_K	223_T	0.511	0.86
188_A	191_K	0.510	0.85
177_F	181_R	0.510	0.85
180_A	202_L	0.509	0.85
189_G	193_R	0.508	0.85
88_N	92_L	0.506	0.85
91_R	118_A	0.504	0.85
78_E	99_W	0.503	0.85
170_E	173_Y	0.502	0.85
54_F	79_W	0.501	0.84
125_V	161_R	0.501	0.84
37_T	223_T	0.500	0.84
205_S	223_T	0.500	0.84

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
3sy1A	1	0.9744	100	0.509	Contact Map
1ct5A	1	0.8846	100	0.516	Contact Map
3cpgA	1	0.9658	100	0.518	Contact Map
3r79A	2	0.953	100	0.522	Contact Map
3e5pA	2	0.9274	100	0.627	Contact Map
4beuA	2	0.9487	100	0.627	Contact Map
4a3qA	2	0.9017	100	0.629	Contact Map
4bf5A	2	0.953	100	0.631	Contact Map
1bd0A	2	0.9188	100	0.634	Contact Map
3kw3A	2	0.9188	100	0.637	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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