YDJI - ECOLI - GREMLIN Contacts

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YDJI - Uncharacterized protein YdjI

UniProt:	P77704	Sequences: MLADIRYWENDATNKHYAIAHFNVWNAEMLMGVIDAAEEAKSPVIISFGTGFVGNTSFEDFSHMMVSMAQKATVPVITHWDHGRSMEIIHNAWTHGMNSLMRDASAFDFEENIRLTKEAVDFFHPLGIPVEAELGHVGNETVYEEALAGYHYTDPDQAAEFVERTGCDSLAVAIGNQHGVYTSEPQLNFEVVKRVRDAVSVPLVLHGASGISDADIKTAISLGIAKINIHTELCQAAMVAVKENQDQPFLHLEREVRKAVKERALEKIKLFGSDGKAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13485
Length:	278 (270)
Sequences:	3946 (2036)
Seq/√Len:	123.9

ECOLI - YDJI GATY KBAY ALF
BACSU - ALF IOLJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
160_E	164_R	3.949	1.00
39_E	265_L	3.306	1.00
39_E	261_K	3.282	1.00
11_D	15_K	3.010	1.00
109_F	160_E	2.863	1.00
42_S	273_S	2.607	1.00
109_F	113_I	2.575	1.00
159_A	163_E	2.554	1.00
40_A	269_K	2.517	1.00
35_D	261_K	2.450	1.00
93_W	128_I	2.430	1.00
193_K	197_D	2.408	1.00
38_E	73_T	2.405	1.00
118_E	121_D	2.365	1.00
90_H	122_F	2.357	1.00
108_D	111_E	2.350	1.00
188_N	191_V	2.300	1.00
33_V	44_V	2.282	1.00
102_R	115_L	2.278	1.00
243_E	247_Q	2.268	1.00
174_I	192_V	2.244	1.00
213_D	270_L	2.219	1.00
48_F	97_M	2.177	1.00
40_A	265_L	2.115	1.00
11_D	17_Y	2.102	1.00
114_R	118_E	2.090	1.00
240_A	259_A	2.021	1.00
5_I	77_I	2.005	1.00
40_A	274_D	1.957	1.00
124_H	168_D	1.947	1.00
189_F	218_T	1.946	1.00
258_K	262_E	1.927	1.00
193_K	222_L	1.926	1.00
8_W	77_I	1.890	1.00
212_S	215_D	1.882	1.00
261_K	265_L	1.851	1.00
10_N	14_N	1.851	1.00
117_K	121_D	1.833	1.00
94_T	122_F	1.790	1.00
159_A	198_A	1.779	1.00
13_T	225_A	1.767	1.00
5_I	169_S	1.767	1.00
6_R	10_N	1.756	1.00
218_T	221_S	1.725	1.00
111_E	114_R	1.722	1.00
90_H	94_T	1.721	1.00
34_I	72_A	1.714	1.00
269_K	274_D	1.706	1.00
104_A	107_F	1.660	1.00
120_V	130_V	1.652	1.00
156_D	198_A	1.616	1.00
21_H	47_S	1.608	1.00
268_I	274_D	1.585	1.00
79_H	99_S	1.555	1.00
94_T	126_L	1.549	1.00
240_A	243_E	1.545	1.00
157_Q	160_E	1.540	1.00
193_K	218_T	1.533	1.00
189_F	222_L	1.513	1.00
24_V	46_I	1.512	1.00
44_V	76_V	1.511	1.00
239_V	243_E	1.485	1.00
110_E	164_R	1.484	1.00
107_F	111_E	1.470	1.00
203_L	224_I	1.466	1.00
31_M	257_R	1.458	1.00
38_E	72_A	1.444	1.00
218_T	222_L	1.432	1.00
34_I	76_V	1.412	1.00
262_E	265_L	1.405	1.00
13_T	196_R	1.402	1.00
194_R	197_D	1.399	1.00
154_D	157_Q	1.382	1.00
122_F	126_L	1.382	1.00
109_F	157_Q	1.361	1.00
30_L	68_M	1.361	1.00
63_H	67_S	1.343	1.00
221_S	272_G	1.335	1.00
66_V	70_Q	1.331	1.00
213_D	266_E	1.330	1.00
86_M	90_H	1.305	1.00
86_M	118_E	1.292	1.00
20_A	264_A	1.291	1.00
176_N	211_I	1.276	1.00
242_K	245_Q	1.255	1.00
259_A	262_E	1.254	1.00
63_H	66_V	1.249	1.00
263_R	266_E	1.246	1.00
35_D	257_R	1.242	0.99
191_V	195_V	1.237	0.99
30_L	65_M	1.234	0.99
41_K	73_T	1.216	0.99
24_V	30_L	1.209	0.99
36_A	264_A	1.208	0.99
36_A	40_A	1.207	0.99
121_D	125_P	1.203	0.99
255_E	258_K	1.201	0.99
50_T	88_I	1.192	0.99
59_E	91_N	1.190	0.99
107_F	115_L	1.182	0.99
24_V	33_V	1.179	0.99
241_V	256_V	1.179	0.99
117_K	164_R	1.177	0.99
220_I	271_F	1.174	0.99
110_E	114_R	1.172	0.99
213_D	217_K	1.164	0.99
116_T	132_A	1.155	0.99
109_F	164_R	1.140	0.99
37_A	44_V	1.138	0.99
16_H	221_S	1.127	0.99
162_V	201_V	1.123	0.99
36_A	261_K	1.122	0.99
230_H	234_C	1.122	0.99
86_M	122_F	1.117	0.99
59_E	71_K	1.115	0.99
110_E	160_E	1.104	0.99
191_V	194_R	1.102	0.99
66_V	78_T	1.100	0.99
194_R	198_A	1.098	0.99
199_V	203_L	1.097	0.99
62_S	78_T	1.094	0.99
100_L	123_F	1.086	0.99
100_L	119_A	1.086	0.99
36_A	265_L	1.082	0.99
119_A	130_V	1.072	0.98
115_L	118_E	1.068	0.98
265_L	269_K	1.059	0.98
87_E	91_N	1.052	0.98
190_E	194_R	1.050	0.98
100_L	130_V	1.049	0.98
113_I	164_R	1.045	0.98
229_I	271_F	1.042	0.98
50_T	85_S	1.038	0.98
32_G	260_V	1.037	0.98
11_D	14_N	1.036	0.98
90_H	126_L	1.032	0.98
262_E	266_E	1.031	0.98
236_A	263_R	1.024	0.98
93_W	122_F	1.024	0.98
93_W	126_L	1.015	0.98
258_K	261_K	1.012	0.98
196_R	225_A	1.011	0.98
7_Y	11_D	1.009	0.98
104_A	115_L	0.994	0.98
20_A	268_I	0.984	0.97
67_S	70_Q	0.976	0.97
139_N	142_V	0.976	0.97
266_E	270_L	0.976	0.97
37_A	268_I	0.973	0.97
227_I	271_F	0.970	0.97
48_F	61_F	0.967	0.97
25_W	52_F	0.964	0.97
20_A	271_F	0.960	0.97
172_V	195_V	0.957	0.97
93_W	123_F	0.956	0.97
190_E	193_K	0.949	0.97
188_N	194_R	0.947	0.97
69_A	72_A	0.946	0.97
30_L	46_I	0.940	0.97
72_A	76_V	0.930	0.96
217_K	221_S	0.930	0.96
158_A	199_V	0.929	0.96
9_E	169_S	0.927	0.96
155_P	198_A	0.927	0.96
205_L	219_A	0.924	0.96
60_D	68_M	0.924	0.96
25_W	29_M	0.920	0.96
241_V	252_L	0.917	0.96
132_A	167_C	0.913	0.96
56_T	61_F	0.913	0.96
98_N	129_P	0.909	0.96
8_W	19_I	0.906	0.96
268_I	273_S	0.903	0.96
16_H	225_A	0.903	0.96
33_V	264_A	0.896	0.95
189_F	215_D	0.896	0.95
132_A	161_F	0.893	0.95
65_M	78_T	0.892	0.95
111_E	115_L	0.889	0.95
152_Y	191_V	0.876	0.95
17_Y	42_S	0.875	0.95
153_T	158_A	0.875	0.95
49_G	52_F	0.866	0.95
180_V	235_Q	0.866	0.95
38_E	74_V	0.863	0.94
174_I	205_L	0.862	0.94
155_P	194_R	0.860	0.94
216_I	227_I	0.851	0.94
216_I	271_F	0.848	0.94
37_A	74_V	0.848	0.94
85_S	88_I	0.841	0.94
248_P	251_H	0.841	0.94
216_I	220_I	0.836	0.93
217_K	272_G	0.834	0.93
49_G	230_H	0.834	0.93
42_S	272_G	0.832	0.93
124_H	127_G	0.829	0.93
62_S	66_V	0.828	0.93
43_P	75_P	0.828	0.93
264_A	268_I	0.826	0.93
22_F	264_A	0.825	0.93
158_A	195_V	0.812	0.92
136_H	150_Y	0.811	0.92
36_A	268_I	0.811	0.92
122_F	125_P	0.810	0.92
22_F	44_V	0.807	0.92
255_E	259_A	0.797	0.92
100_L	128_I	0.793	0.92
7_Y	10_N	0.791	0.91
242_K	246_D	0.787	0.91
84_R	106_A	0.787	0.91
48_F	53_V	0.787	0.91
116_T	120_V	0.786	0.91
26_N	29_M	0.786	0.91
160_E	163_E	0.785	0.91
240_A	256_V	0.779	0.91
47_S	230_H	0.777	0.91
134_L	162_V	0.775	0.91
268_I	275_G	0.773	0.90
244_N	247_Q	0.772	0.90
243_E	246_D	0.768	0.90
27_A	64_M	0.767	0.90
102_R	119_A	0.764	0.90
9_E	19_I	0.763	0.90
217_K	270_L	0.763	0.90
47_S	79_H	0.758	0.90
52_F	230_H	0.758	0.90
119_A	122_F	0.756	0.89
49_G	250_L	0.754	0.89
108_D	114_R	0.753	0.89
156_D	159_A	0.752	0.89
162_V	199_V	0.750	0.89
85_S	89_I	0.747	0.89
5_I	129_P	0.746	0.89
22_F	33_V	0.744	0.89
62_S	97_M	0.741	0.89
23_N	49_G	0.740	0.88
123_F	128_I	0.734	0.88
120_V	124_H	0.733	0.88
212_S	216_I	0.731	0.88
232_E	267_K	0.730	0.88
192_V	224_I	0.725	0.87
237_A	253_E	0.725	0.87
41_K	275_G	0.724	0.87
145_E	150_Y	0.721	0.87
153_T	172_V	0.711	0.86
92_A	97_M	0.710	0.86
176_N	187_L	0.705	0.86
134_L	161_F	0.705	0.86
237_A	256_V	0.700	0.86
233_L	260_V	0.699	0.85
13_T	200_S	0.696	0.85
192_V	222_L	0.696	0.85
120_V	166_G	0.694	0.85
172_V	192_V	0.692	0.85
195_V	199_V	0.691	0.85
9_E	129_P	0.687	0.84
25_W	230_H	0.686	0.84
25_W	49_G	0.684	0.84
153_T	195_V	0.678	0.84
155_P	191_V	0.678	0.84
260_V	264_A	0.677	0.84
22_F	268_I	0.674	0.83
10_N	13_T	0.673	0.83
245_Q	252_L	0.673	0.83
8_W	11_D	0.672	0.83
238_M	245_Q	0.672	0.83
5_I	8_W	0.671	0.83
240_A	244_N	0.671	0.83
28_E	237_A	0.668	0.83
220_I	223_G	0.668	0.83
149_G	154_D	0.667	0.83
181_Y	223_G	0.664	0.82
77_I	129_P	0.664	0.82
169_S	204_V	0.664	0.82
147_L	150_Y	0.659	0.82
134_L	158_A	0.659	0.82
51_G	250_L	0.659	0.82
152_Y	188_N	0.658	0.82
214_A	217_K	0.657	0.82
109_F	134_L	0.656	0.82
214_A	218_T	0.652	0.81
240_A	255_E	0.651	0.81
254_R	258_K	0.650	0.81
102_R	107_F	0.649	0.81
24_V	61_F	0.649	0.81
91_N	95_H	0.645	0.81
45_I	77_I	0.645	0.81
5_I	45_I	0.643	0.80
244_N	255_E	0.642	0.80
31_M	35_D	0.642	0.80
197_D	200_S	0.637	0.80
181_Y	185_P	0.636	0.80
69_A	76_V	0.632	0.79
57_S	60_D	0.632	0.79
83_G	89_I	0.631	0.79
42_S	275_G	0.629	0.79
216_I	229_I	0.623	0.78
17_Y	272_G	0.623	0.78
53_V	88_I	0.621	0.78
144_E	147_L	0.619	0.78
130_V	167_C	0.617	0.78
34_I	46_I	0.615	0.77
50_T	84_R	0.611	0.77
162_V	167_C	0.609	0.77
67_S	71_K	0.607	0.76
138_G	208_A	0.606	0.76
167_C	201_V	0.606	0.76
235_Q	239_V	0.605	0.76
5_I	9_E	0.602	0.76
62_S	95_H	0.601	0.76
34_I	74_V	0.601	0.76
132_A	165_T	0.596	0.75
263_R	267_K	0.596	0.75
38_E	41_K	0.592	0.75
86_M	119_A	0.591	0.75
115_L	119_A	0.590	0.74
66_V	69_A	0.589	0.74
266_E	269_K	0.588	0.74
174_I	222_L	0.587	0.74
25_W	249_F	0.586	0.74
86_M	89_I	0.585	0.74
183_S	231_T	0.583	0.74
89_I	119_A	0.581	0.73
177_Q	185_P	0.579	0.73
113_I	160_E	0.579	0.73
229_I	232_E	0.575	0.73
209_S	232_E	0.574	0.72
216_I	270_L	0.574	0.72
23_N	55_N	0.573	0.72
14_N	194_R	0.573	0.72
32_G	257_R	0.571	0.72
140_E	147_L	0.571	0.72
93_W	100_L	0.570	0.72
129_P	169_S	0.569	0.72
42_S	268_I	0.569	0.72
196_R	200_S	0.568	0.72
251_H	255_E	0.567	0.72
154_D	191_V	0.566	0.71
25_W	48_F	0.566	0.71
64_M	67_S	0.565	0.71
58_F	91_N	0.562	0.71
112_N	135_G	0.562	0.71
32_G	36_A	0.561	0.71
12_A	17_Y	0.561	0.71
104_A	132_A	0.561	0.71
187_L	219_A	0.561	0.71
61_F	64_M	0.560	0.71
16_H	196_R	0.559	0.70
77_I	98_N	0.558	0.70
217_K	220_I	0.558	0.70
26_N	249_F	0.555	0.70
61_F	65_M	0.554	0.70
88_I	91_N	0.553	0.70
153_T	161_F	0.551	0.69
195_V	203_L	0.551	0.69
30_L	64_M	0.550	0.69
27_A	56_T	0.548	0.69
134_L	154_D	0.546	0.69
5_I	98_N	0.543	0.68
110_E	113_I	0.542	0.68
113_I	165_T	0.540	0.68
14_N	247_Q	0.539	0.68
52_F	248_P	0.538	0.68
157_Q	164_R	0.537	0.67
241_V	253_E	0.536	0.67
208_A	229_I	0.534	0.67
254_R	257_R	0.533	0.67
87_E	90_H	0.531	0.67
144_E	150_Y	0.530	0.66
215_D	218_T	0.529	0.66
78_T	98_N	0.527	0.66
62_S	69_A	0.527	0.66
224_I	227_I	0.527	0.66
132_A	154_D	0.525	0.66
29_M	52_F	0.524	0.66
90_H	125_P	0.523	0.65
136_H	191_V	0.522	0.65
19_I	129_P	0.522	0.65
249_F	252_L	0.520	0.65
72_A	75_P	0.517	0.65
156_D	160_E	0.516	0.64
174_I	219_A	0.516	0.64
116_T	165_T	0.515	0.64
44_V	268_I	0.514	0.64
229_I	267_K	0.513	0.64
84_R	88_I	0.513	0.64
114_R	164_R	0.512	0.64
258_K	269_K	0.512	0.64
180_V	232_E	0.512	0.64
144_E	148_A	0.511	0.64
109_F	170_L	0.511	0.64
36_A	44_V	0.509	0.63
117_K	120_V	0.507	0.63
234_C	249_F	0.507	0.63
131_E	226_K	0.506	0.63
8_W	225_A	0.504	0.63
93_W	124_H	0.504	0.63
51_G	248_P	0.504	0.63
253_E	256_V	0.504	0.63
49_G	55_N	0.503	0.62
29_M	260_V	0.503	0.62
234_C	238_M	0.501	0.62
20_A	47_S	0.500	0.62
163_E	200_S	0.500	0.62

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
1gvfA	3	0.9748	100	0.048	Contact Map
3n9rA	3	0.964	100	0.049	Contact Map
1rvgA	3	0.9928	100	0.053	Contact Map
4to8A	2	0.9748	100	0.058	Contact Map
2iswA	2	0.9496	100	0.06	Contact Map
3pm6A	2	0.9856	100	0.098	Contact Map
3elfA	4	0.9568	100	0.098	Contact Map
1dosA	2	0.9424	100	0.114	Contact Map
3qm3A	4	0.9784	100	0.118	Contact Map
3txvA	2	0.8813	100	0.241	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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