FOLD - HALSA - GREMLIN Contacts

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FOLD - Bifunctional protein FolD

UniProt:	Q9HPY4	Sequences: MTEIIDGDAVAAQLRADLTGAVETLETAGVTPRLATVLMNDKQASETYVSMKQQDCEEVGIAAEDVRIDPEASADTLFDTVAELNAREDVHGILVQDPTPDHVPDERVLSAVDPAKDVDGFHPENVGKLVGGTPRFKPCTPHGVQKLLAHQGVDPDGAEVVVVGRSNIVGKPLANLLAQKAAGGNATVTICHSHTDDLAAHTRRADVVVAACGVPELIDGDMLSGDPVVIDVGINRVDADTEKGYELVGDVDYDSAEAAASAITPVPGGVGPMTRAMLLYNTLAAASEQTGVAVALP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	297 (278)
Sequences:	4766 (2939)
Seq/√Len:	176.2

ECOLI - FOLD
BACSU - FOLD
HALSA - FOLD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_A	287_S	4.061	1.00
149_A	180_K	3.493	1.00
82_A	111_A	3.193	1.00
91_H	289_Q	3.141	1.00
159_E	204_R	3.128	1.00
252_D	255_S	3.061	1.00
74_A	107_R	2.992	1.00
197_D	200_A	2.884	1.00
80_T	83_E	2.657	1.00
13_Q	150_H	2.650	1.00
159_E	201_H	2.618	1.00
163_V	218_I	2.530	1.00
6_D	9_A	2.527	1.00
33_R	64_E	2.401	1.00
78_F	111_A	2.336	1.00
156_D	185_N	2.230	1.00
30_V	91_H	2.217	1.00
212_C	217_L	2.209	1.00
225_G	259_A	2.145	1.00
216_E	252_D	2.107	1.00
55_D	275_R	2.105	1.00
66_V	80_T	2.099	1.00
208_V	223_L	2.095	1.00
72_A	77_L	2.065	1.00
82_A	86_A	2.054	1.00
15_R	58_E	2.051	1.00
237_V	245_Y	2.022	1.00
220_G	255_S	2.012	1.00
121_F	168_I	1.963	1.00
174_A	190_I	1.925	1.00
219_D	222_M	1.891	1.00
26_E	31_T	1.871	1.00
228_V	261_S	1.865	1.00
146_K	149_A	1.860	1.00
160_V	177_L	1.855	1.00
136_F	285_A	1.852	1.00
223_L	256_A	1.838	1.00
95_V	108_V	1.826	1.00
4_I	253_Y	1.823	1.00
155_P	207_V	1.800	1.00
145_Q	180_K	1.786	1.00
253_Y	263_I	1.778	1.00
33_R	62_A	1.771	1.00
202_T	208_V	1.727	1.00
41_D	46_E	1.724	1.00
47_T	247_L	1.717	1.00
237_V	246_E	1.683	1.00
156_D	194_H	1.669	1.00
19_T	23_E	1.663	1.00
199_A	203_R	1.641	1.00
146_K	280_Y	1.633	1.00
18_L	283_L	1.624	1.00
201_H	204_R	1.582	1.00
59_V	279_L	1.580	1.00
206_D	224_S	1.552	1.00
10_V	151_Q	1.547	1.00
130_V	175_N	1.511	1.00
137_K	176_L	1.495	1.00
219_D	252_D	1.486	1.00
158_A	196_D	1.482	1.00
251_V	256_A	1.471	1.00
178_A	190_I	1.468	1.00
239_A	246_E	1.461	1.00
38_L	46_E	1.442	1.00
229_V	251_V	1.440	1.00
208_V	218_I	1.434	1.00
146_K	277_M	1.416	1.00
146_K	150_H	1.406	1.00
162_V	173_L	1.402	1.00
68_I	72_A	1.396	1.00
202_T	222_M	1.394	1.00
15_R	55_D	1.391	1.00
284_A	288_E	1.375	1.00
154_D	158_A	1.354	1.00
161_V	191_C	1.341	1.00
74_A	78_F	1.340	1.00
74_A	104_P	1.340	1.00
18_L	59_V	1.334	1.00
64_E	90_V	1.323	1.00
17_D	150_H	1.321	1.00
200_A	204_R	1.313	1.00
47_T	51_M	1.310	1.00
3_E	262_A	1.295	1.00
142_H	280_Y	1.295	1.00
219_D	255_S	1.291	1.00
68_I	80_T	1.284	1.00
220_G	259_A	1.281	1.00
254_D	257_E	1.278	1.00
165_R	185_N	1.275	1.00
220_G	256_A	1.274	1.00
142_H	284_A	1.274	1.00
62_A	90_V	1.265	1.00
41_D	70_P	1.261	1.00
191_C	201_H	1.251	1.00
20_G	23_E	1.249	1.00
10_V	150_H	1.247	1.00
73_S	76_T	1.229	1.00
24_T	28_A	1.227	1.00
153_V	262_A	1.224	1.00
165_R	193_S	1.224	1.00
224_S	227_P	1.214	1.00
5_I	151_Q	1.211	1.00
14_L	18_L	1.209	1.00
216_E	248_V	1.206	1.00
161_V	205_A	1.199	1.00
22_V	61_I	1.196	1.00
53_Q	57_E	1.192	1.00
191_C	195_T	1.191	1.00
191_C	198_L	1.186	1.00
239_A	245_Y	1.179	1.00
35_A	66_V	1.168	1.00
97_D	109_L	1.167	1.00
53_Q	65_D	1.155	1.00
8_D	12_A	1.152	1.00
71_E	76_T	1.145	1.00
223_L	227_P	1.142	1.00
104_P	107_R	1.138	1.00
50_S	54_Q	1.125	1.00
203_R	259_A	1.117	1.00
126_V	130_V	1.107	1.00
161_V	201_H	1.107	1.00
64_E	87_R	1.106	1.00
35_A	90_V	1.104	1.00
38_L	67_R	1.100	1.00
185_N	194_H	1.100	1.00
216_E	254_D	1.099	1.00
61_I	283_L	1.098	1.00
62_A	89_D	1.095	1.00
12_A	16_A	1.087	1.00
24_T	27_T	1.079	1.00
74_A	103_V	1.077	1.00
16_A	19_T	1.073	1.00
199_A	222_M	1.067	1.00
16_A	20_G	1.053	1.00
212_C	235_N	1.052	1.00
35_A	84_L	1.050	1.00
23_E	27_T	1.050	1.00
214_V	217_L	1.038	0.99
237_V	248_V	1.015	0.99
5_I	10_V	1.010	0.99
46_E	67_R	1.010	0.99
143_G	273_M	1.009	0.99
158_A	207_V	1.008	0.99
9_A	13_Q	1.007	0.99
256_A	263_I	1.005	0.99
199_A	221_D	1.005	0.99
41_D	67_R	0.998	0.99
30_V	286_A	0.982	0.99
128_K	133_T	0.980	0.99
75_D	79_D	0.979	0.99
5_I	262_A	0.975	0.99
37_V	84_L	0.970	0.99
160_V	186_A	0.965	0.99
31_T	62_A	0.963	0.99
20_G	24_T	0.957	0.99
238_D	245_Y	0.956	0.99
187_T	195_T	0.954	0.99
215_P	237_V	0.945	0.99
56_C	279_L	0.943	0.99
110_S	123_P	0.939	0.99
56_C	61_I	0.937	0.99
78_F	107_R	0.935	0.99
55_D	59_V	0.933	0.99
142_H	146_K	0.932	0.99
49_V	96_Q	0.928	0.99
85_N	113_D	0.923	0.99
14_L	276_A	0.921	0.99
79_D	83_E	0.920	0.99
46_E	50_S	0.919	0.99
55_D	279_L	0.913	0.99
193_S	212_C	0.913	0.99
57_E	62_A	0.912	0.99
148_L	151_Q	0.911	0.99
144_V	232_V	0.905	0.99
163_V	212_C	0.902	0.99
255_S	258_A	0.901	0.99
151_Q	262_A	0.899	0.99
171_K	178_A	0.897	0.99
78_F	82_A	0.894	0.98
66_V	83_E	0.884	0.98
15_R	276_A	0.879	0.98
189_T	201_H	0.876	0.98
76_T	79_D	0.875	0.98
103_V	108_V	0.872	0.98
18_L	276_A	0.870	0.98
272_P	275_R	0.870	0.98
83_E	87_R	0.869	0.98
155_P	186_A	0.868	0.98
134_P	284_A	0.866	0.98
163_V	208_V	0.864	0.98
91_H	286_A	0.861	0.98
33_R	90_V	0.860	0.98
34_L	118_V	0.857	0.98
137_K	142_H	0.856	0.98
10_V	13_Q	0.852	0.98
21_A	283_L	0.852	0.98
10_V	147_L	0.850	0.98
147_L	273_M	0.848	0.98
17_D	280_Y	0.846	0.98
132_G	171_K	0.843	0.98
8_D	268_G	0.842	0.98
36_T	63_A	0.835	0.98
84_L	93_I	0.834	0.98
25_L	29_G	0.833	0.98
218_I	222_M	0.830	0.98
185_N	192_H	0.829	0.98
14_L	277_M	0.825	0.97
185_N	193_S	0.824	0.97
167_N	171_K	0.824	0.97
145_Q	155_P	0.824	0.97
147_L	264_T	0.823	0.97
253_Y	257_E	0.821	0.97
139_C	277_M	0.820	0.97
78_F	108_V	0.818	0.97
54_Q	58_E	0.818	0.97
228_V	262_A	0.818	0.97
53_Q	67_R	0.813	0.97
210_A	235_N	0.804	0.97
145_Q	149_A	0.802	0.97
72_A	80_T	0.801	0.97
51_M	54_Q	0.801	0.97
95_V	112_V	0.798	0.97
124_E	128_K	0.791	0.97
129_L	137_K	0.784	0.97
199_A	202_T	0.782	0.96
66_V	84_L	0.782	0.96
35_A	64_E	0.780	0.96
159_E	196_D	0.780	0.96
215_P	234_I	0.772	0.96
285_A	289_Q	0.771	0.96
13_Q	17_D	0.765	0.96
256_A	259_A	0.764	0.96
5_I	230_I	0.761	0.96
200_A	203_R	0.760	0.96
163_V	210_A	0.754	0.96
210_A	251_V	0.752	0.96
122_H	125_N	0.750	0.96
216_E	237_V	0.749	0.96
209_V	232_V	0.747	0.95
159_E	189_T	0.744	0.95
106_E	133_T	0.743	0.95
142_H	277_M	0.740	0.95
17_D	20_G	0.738	0.95
18_L	22_V	0.737	0.95
145_Q	160_V	0.734	0.95
226_D	260_A	0.729	0.95
12_A	58_E	0.718	0.94
235_N	248_V	0.714	0.94
215_P	248_V	0.712	0.94
144_V	230_I	0.707	0.94
77_L	108_V	0.706	0.94
22_V	25_L	0.706	0.94
61_I	279_L	0.706	0.94
78_F	103_V	0.704	0.94
47_T	234_I	0.702	0.94
236_R	247_L	0.701	0.94
25_L	30_V	0.696	0.93
81_V	108_V	0.694	0.93
17_D	146_K	0.694	0.93
162_V	188_V	0.693	0.93
77_L	103_V	0.691	0.93
51_M	275_R	0.686	0.93
124_E	135_R	0.685	0.93
69_D	72_A	0.685	0.93
36_T	53_Q	0.683	0.93
11_A	15_R	0.677	0.92
23_E	26_E	0.673	0.92
39_M	77_L	0.673	0.92
165_R	192_H	0.671	0.92
21_A	280_Y	0.671	0.92
84_L	90_V	0.670	0.92
227_P	261_S	0.669	0.92
110_S	128_K	0.663	0.92
52_K	96_Q	0.662	0.92
156_D	196_D	0.662	0.92
88_E	289_Q	0.660	0.91
13_Q	16_A	0.659	0.91
106_E	110_S	0.658	0.91
93_I	112_V	0.656	0.91
277_M	280_Y	0.647	0.91
26_E	30_V	0.646	0.91
17_D	21_A	0.646	0.91
47_T	50_S	0.645	0.91
280_Y	284_A	0.645	0.91
214_V	219_D	0.645	0.91
160_V	173_L	0.643	0.90
18_L	21_A	0.643	0.90
114_P	122_H	0.641	0.90
51_M	234_I	0.641	0.90
218_I	223_L	0.640	0.90
162_V	177_L	0.638	0.90
210_A	218_I	0.635	0.90
148_L	153_V	0.633	0.90
25_L	286_A	0.633	0.90
56_C	63_A	0.632	0.90
229_V	256_A	0.631	0.90
173_L	209_V	0.630	0.89
37_V	80_T	0.629	0.89
25_L	283_L	0.627	0.89
97_D	121_F	0.625	0.89
254_D	258_A	0.624	0.89
97_D	105_D	0.624	0.89
47_T	236_R	0.623	0.89
141_P	173_L	0.623	0.89
10_V	146_K	0.623	0.89
76_T	80_T	0.621	0.89
44_A	236_R	0.620	0.89
231_D	249_G	0.619	0.89
175_N	178_A	0.618	0.89
226_D	261_S	0.617	0.88
147_L	272_P	0.615	0.88
153_V	228_V	0.613	0.88
81_V	85_N	0.613	0.88
161_V	202_T	0.611	0.88
227_P	260_A	0.610	0.88
153_V	207_V	0.606	0.88
22_V	29_G	0.602	0.87
7_G	11_A	0.601	0.87
72_A	103_V	0.601	0.87
49_V	52_K	0.600	0.87
107_R	111_A	0.600	0.87
177_L	209_V	0.599	0.87
53_Q	63_A	0.598	0.87
77_L	99_T	0.596	0.87
123_P	126_V	0.595	0.87
110_S	133_T	0.593	0.86
54_Q	57_E	0.593	0.86
187_T	191_C	0.593	0.86
123_P	131_G	0.591	0.86
6_D	268_G	0.590	0.86
22_V	26_E	0.589	0.86
25_L	31_T	0.589	0.86
199_A	219_D	0.589	0.86
165_R	194_H	0.586	0.86
118_V	285_A	0.586	0.86
166_S	266_V	0.586	0.86
22_V	59_V	0.585	0.86
193_S	214_V	0.584	0.86
156_D	193_S	0.583	0.86
64_E	89_D	0.583	0.86
9_A	12_A	0.579	0.85
208_V	229_V	0.578	0.85
52_K	272_P	0.578	0.85
3_E	151_Q	0.577	0.85
223_L	260_A	0.576	0.85
155_P	180_K	0.576	0.85
115_A	289_Q	0.574	0.85
230_I	270_V	0.574	0.85
12_A	15_R	0.574	0.85
19_T	58_E	0.573	0.85
36_T	65_D	0.573	0.85
14_L	280_Y	0.572	0.84
79_D	82_A	0.572	0.84
163_V	202_T	0.570	0.84
279_L	282_T	0.569	0.84
161_V	208_V	0.566	0.84
148_L	155_P	0.566	0.84
164_G	233_G	0.565	0.84
43_Q	47_T	0.565	0.84
15_R	59_V	0.562	0.83
38_L	49_V	0.562	0.83
21_A	24_T	0.561	0.83
178_A	192_H	0.558	0.83
57_E	61_I	0.557	0.83
169_V	173_L	0.556	0.83
257_E	263_I	0.555	0.83
5_I	150_H	0.555	0.83
132_G	179_Q	0.552	0.82
39_M	99_T	0.550	0.82
96_Q	275_R	0.547	0.82
158_A	228_V	0.545	0.82
215_P	235_N	0.543	0.81
251_V	263_I	0.543	0.81
45_S	96_Q	0.542	0.81
203_R	221_D	0.542	0.81
193_S	217_L	0.540	0.81
126_V	131_G	0.540	0.81
125_N	135_R	0.540	0.81
118_V	282_T	0.539	0.81
22_V	283_L	0.539	0.81
16_A	58_E	0.537	0.81
14_L	146_K	0.536	0.80
171_K	179_Q	0.535	0.80
115_A	288_E	0.531	0.80
121_F	126_V	0.528	0.79
147_L	270_V	0.527	0.79
37_V	81_V	0.526	0.79
86_A	113_D	0.525	0.79
234_I	266_V	0.525	0.79
131_G	167_N	0.521	0.79
28_A	86_A	0.520	0.78
33_R	89_D	0.519	0.78
114_P	124_E	0.518	0.78
66_V	72_A	0.517	0.78
220_G	258_A	0.517	0.78
234_I	247_L	0.516	0.78
78_F	85_N	0.514	0.78
7_G	272_P	0.512	0.77
43_Q	236_R	0.511	0.77
36_T	52_K	0.511	0.77
35_A	65_D	0.511	0.77
26_E	29_G	0.511	0.77
202_T	218_I	0.510	0.77
129_L	134_P	0.509	0.77
115_A	128_K	0.508	0.77
202_T	223_L	0.508	0.77
151_Q	228_V	0.507	0.77
37_V	66_V	0.505	0.76
225_G	261_S	0.505	0.76
153_V	158_A	0.504	0.76
231_D	267_P	0.504	0.76
128_K	131_G	0.503	0.76
55_D	58_E	0.503	0.76
129_L	135_R	0.502	0.76
234_I	237_V	0.502	0.76
52_K	275_R	0.500	0.76
99_T	103_V	0.500	0.76

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
4cjxA	2	0.9697	100	0.299	Contact Map
3l07A	2	0.9461	100	0.307	Contact Map
4a5oA	2	0.9495	100	0.314	Contact Map
2c2xA	2	0.9428	100	0.314	Contact Map
4a26A	2	0.9731	100	0.318	Contact Map
1b0aA	2	0.963	100	0.321	Contact Map
3p2oA	2	0.9428	100	0.331	Contact Map
4b4uA	2	0.9461	100	0.337	Contact Map
1a4iA	2	0.9663	100	0.351	Contact Map
1edzA	2	0.9057	100	0.431	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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