YDHJ - ECOLI - GREMLIN Contacts

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YDHJ - Uncharacterized protein YdhJ

UniProt:	P76185	Sequences: MSIKTIKYFSTIIVAVVAVLAGWWLWNYYMQSPWTRDGKIRAEQVSITPQVSGRIVELNIKDNQLVNAGDLLLTIDKTPFQIAELNAQAQLAKAQSDLAKANNEANRRRHLSQNFISAEELDTANLNVKAMQASVDAAQATLKQAQWQLAQTEIRAPVSGWVTNLTTRIGDYADTGKPLFALVDSHSFYVIGYFEETKLRHIREGAPAQITLYSDNKTLQGHVSSIGRAIYDQSVESDSSLIPDVKPNVPWVRLAQRVPVRFALDKVPGDVTLVSGTTCSIAVGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13944
Length:	285 (261)
Sequences:	30013 (24201)
Seq/√Len:	1498.0

ECOLI - YDHJ AAEA YHII EMRK EMRA MDTN ACRA ACRE YBHG YIBH MACA YIAV MDTA MDTE CUSB
BACSU - YVRP YKNX YHBJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_E	74_T	3.244	1.00
71_L	153_E	3.130	1.00
67_N	159_S	2.778	1.00
59_N	74_T	2.476	1.00
74_T	153_E	2.468	1.00
41_R	191_I	2.446	1.00
108_R	116_I	2.336	1.00
207_P	220_Q	2.320	1.00
50_Q	151_Q	2.301	1.00
77_K	81_Q	2.247	1.00
65_L	161_W	2.209	1.00
108_R	124_A	2.192	1.00
71_L	155_R	2.182	1.00
67_N	70_D	2.167	1.00
59_N	71_L	2.033	1.00
192_G	260_V	2.028	1.00
163_T	183_V	2.007	1.00
209_Q	220_Q	2.002	1.00
128_V	132_Q	1.912	1.00
209_Q	218_T	1.882	1.00
109_R	112_S	1.847	1.00
68_A	159_S	1.816	1.00
125_N	129_K	1.807	1.00
88_Q	146_Q	1.785	1.00
105_A	109_R	1.748	1.00
136_D	139_Q	1.743	1.00
191_I	240_S	1.742	1.00
85_L	88_Q	1.713	1.00
102_N	106_N	1.708	1.00
118_A	122_D	1.701	1.00
120_E	123_T	1.686	1.00
46_S	178_P	1.682	1.00
174_D	177_K	1.666	1.00
92_A	95_Q	1.660	1.00
105_A	121_L	1.642	1.00
217_K	251_W	1.628	1.00
129_K	132_Q	1.623	1.00
109_R	125_N	1.609	1.00
61_K	64_Q	1.606	1.00
40_I	190_V	1.581	1.00
135_V	139_Q	1.565	1.00
84_E	88_Q	1.536	1.00
84_E	146_Q	1.531	1.00
207_P	222_H	1.528	1.00
81_Q	85_L	1.519	1.00
143_K	146_Q	1.496	1.00
43_E	184_D	1.492	1.00
55_I	73_L	1.484	1.00
144_Q	148_Q	1.472	1.00
23_W	27_N	1.471	1.00
23_W	26_W	1.468	1.00
190_V	258_V	1.448	1.00
71_L	74_T	1.440	1.00
91_L	95_Q	1.437	1.00
81_Q	149_L	1.433	1.00
121_L	125_N	1.430	1.00
56_V	76_D	1.403	1.00
80_F	152_T	1.401	1.00
55_I	167_T	1.393	1.00
86_N	141_T	1.384	1.00
105_A	125_N	1.383	1.00
195_E	198_K	1.382	1.00
224_S	242_I	1.377	1.00
53_G	75_I	1.372	1.00
44_Q	181_A	1.371	1.00
209_Q	263_A	1.371	1.00
99_A	103_N	1.368	1.00
46_S	181_A	1.367	1.00
184_D	187_S	1.355	1.00
52_S	175_T	1.354	1.00
56_V	74_T	1.348	1.00
142_L	146_Q	1.343	1.00
65_L	185_S	1.337	1.00
98_L	102_N	1.333	1.00
35_T	261_R	1.332	1.00
95_Q	139_Q	1.325	1.00
100_K	104_E	1.323	1.00
73_L	154_I	1.315	1.00
93_K	134_S	1.314	1.00
119_E	123_T	1.314	1.00
93_K	97_D	1.301	1.00
224_S	244_D	1.290	1.00
60_I	70_D	1.288	1.00
106_N	109_R	1.280	1.00
88_Q	142_L	1.279	1.00
83_A	148_Q	1.277	1.00
212_L	258_V	1.277	1.00
127_N	130_A	1.273	1.00
134_S	137_A	1.263	1.00
164_N	181_A	1.259	1.00
91_L	142_L	1.250	1.00
147_W	151_Q	1.249	1.00
35_T	259_P	1.249	1.00
162_V	180_F	1.249	1.00
22_G	26_W	1.247	1.00
99_A	102_N	1.241	1.00
83_A	86_N	1.235	1.00
104_E	123_T	1.232	1.00
139_Q	143_K	1.225	1.00
88_Q	92_A	1.224	1.00
57_E	169_I	1.223	1.00
109_R	121_L	1.217	1.00
106_N	110_H	1.217	1.00
102_N	128_V	1.212	1.00
102_N	132_Q	1.207	1.00
211_T	218_T	1.206	1.00
83_A	144_Q	1.202	1.00
211_T	261_R	1.200	1.00
95_Q	135_V	1.198	1.00
189_Y	242_I	1.196	1.00
86_N	90_Q	1.194	1.00
165_L	168_R	1.192	1.00
90_Q	93_K	1.191	1.00
98_L	128_V	1.190	1.00
107_R	122_D	1.184	1.00
72_L	180_F	1.181	1.00
61_K	165_L	1.179	1.00
209_Q	261_R	1.174	1.00
84_E	142_L	1.170	1.00
50_Q	54_R	1.156	1.00
77_K	152_T	1.152	1.00
110_H	113_Q	1.139	1.00
231_Y	234_S	1.126	1.00
221_G	243_P	1.123	1.00
20_L	24_W	1.108	1.00
98_L	132_Q	1.104	1.00
95_Q	99_A	1.103	1.00
45_V	158_V	1.102	1.00
62_D	164_N	1.099	1.00
123_T	127_N	1.098	1.00
105_A	128_V	1.097	1.00
91_L	139_Q	1.094	1.00
137_A	141_T	1.092	1.00
49_P	154_I	1.082	1.00
40_I	188_F	1.080	1.00
127_N	131_M	1.080	1.00
222_H	244_D	1.071	1.00
77_K	153_E	1.065	1.00
97_D	100_K	1.063	1.00
203_R	206_A	1.060	1.00
187_S	244_D	1.052	1.00
190_V	210_I	1.051	1.00
104_E	108_R	1.051	1.00
21_A	25_L	1.045	1.00
73_L	180_F	1.045	1.00
90_Q	141_T	1.044	1.00
247_P	250_P	1.043	1.00
94_A	97_D	1.041	1.00
122_D	125_N	1.033	1.00
156_A	182_L	1.033	1.00
100_K	103_N	1.031	1.00
90_Q	94_A	1.025	1.00
97_D	134_S	1.021	1.00
210_I	221_G	1.016	1.00
91_L	135_V	1.013	1.00
138_A	141_T	1.012	1.00
65_L	159_S	1.009	1.00
146_Q	150_A	0.997	1.00
60_I	180_F	0.993	1.00
160_G	182_L	0.992	1.00
85_L	143_K	0.990	1.00
132_Q	136_D	0.990	1.00
141_T	144_Q	0.988	1.00
230_I	239_S	0.988	1.00
52_S	174_D	0.985	1.00
73_L	179_L	0.973	1.00
173_A	179_L	0.972	1.00
267_V	270_D	0.961	1.00
94_A	138_A	0.957	1.00
190_V	260_V	0.956	1.00
98_L	135_V	0.954	1.00
54_R	172_Y	0.951	1.00
192_G	241_L	0.950	1.00
104_E	119_E	0.946	1.00
40_I	252_V	0.942	1.00
108_R	120_E	0.940	1.00
227_G	240_S	0.938	1.00
97_D	130_A	0.935	1.00
193_Y	238_D	0.934	1.00
19_V	23_W	0.933	1.00
79_P	83_A	0.932	1.00
38_G	258_V	0.927	1.00
74_T	77_K	0.925	1.00
58_L	73_L	0.925	1.00
84_E	149_L	0.925	1.00
58_L	169_I	0.919	1.00
166_T	181_A	0.911	1.00
55_I	173_A	0.905	1.00
145_A	148_Q	0.897	1.00
211_T	259_P	0.894	1.00
26_W	29_Y	0.889	1.00
60_I	165_L	0.887	1.00
198_K	201_H	0.883	1.00
166_T	178_P	0.882	1.00
101_A	131_M	0.874	1.00
165_L	180_F	0.873	1.00
26_W	30_M	0.869	1.00
156_A	159_S	0.868	1.00
49_P	73_L	0.865	1.00
111_L	114_N	0.864	1.00
64_Q	70_D	0.862	1.00
95_Q	98_L	0.862	1.00
36_R	192_G	0.857	1.00
189_Y	224_S	0.856	1.00
87_A	138_A	0.853	1.00
114_N	118_A	0.853	1.00
73_L	165_L	0.848	1.00
56_V	59_N	0.848	1.00
47_I	157_P	0.841	1.00
40_I	258_V	0.840	1.00
99_A	129_K	0.835	1.00
51_V	80_F	0.833	1.00
50_Q	79_P	0.829	1.00
194_F	202_I	0.829	1.00
125_N	128_V	0.827	1.00
134_S	138_A	0.825	1.00
130_A	134_S	0.825	1.00
62_D	165_L	0.823	1.00
103_N	122_D	0.820	1.00
78_T	147_W	0.819	1.00
192_G	243_P	0.815	1.00
147_W	150_A	0.814	1.00
49_P	173_A	0.813	1.00
253_R	256_Q	0.802	1.00
60_I	162_V	0.800	1.00
22_G	25_L	0.797	1.00
56_V	77_K	0.796	1.00
158_V	182_L	0.794	1.00
92_A	136_D	0.793	1.00
42_A	254_L	0.792	1.00
208_A	243_P	0.790	1.00
87_A	90_Q	0.785	1.00
43_E	168_R	0.783	1.00
140_A	143_K	0.782	1.00
208_A	221_G	0.780	1.00
116_I	120_E	0.779	1.00
210_I	243_P	0.778	1.00
65_L	250_P	0.777	1.00
263_A	266_K	0.776	1.00
103_N	106_N	0.770	1.00
138_A	142_L	0.769	1.00
100_K	126_L	0.765	1.00
90_Q	137_A	0.761	1.00
223_V	241_L	0.758	1.00
211_T	216_N	0.755	1.00
97_D	101_A	0.752	1.00
100_K	123_T	0.751	1.00
52_S	172_Y	0.750	1.00
161_W	185_S	0.744	1.00
192_G	262_F	0.742	1.00
44_Q	183_V	0.739	1.00
143_K	147_W	0.728	1.00
82_I	147_W	0.726	1.00
136_D	140_A	0.726	1.00
111_L	115_F	0.723	1.00
36_R	194_F	0.723	1.00
188_F	254_L	0.723	1.00
225_S	242_I	0.719	1.00
46_S	171_D	0.715	1.00
82_I	140_A	0.713	1.00
221_G	241_L	0.713	1.00
45_V	157_P	0.712	1.00
66_V	72_L	0.708	1.00
144_Q	147_W	0.705	1.00
21_A	24_W	0.705	1.00
68_A	157_P	0.689	1.00
54_R	76_D	0.687	1.00
25_L	28_Y	0.685	1.00
90_Q	134_S	0.685	1.00
210_I	260_V	0.684	1.00
108_R	119_E	0.683	1.00
207_P	263_A	0.680	1.00
199_L	237_S	0.679	1.00
87_A	145_A	0.678	1.00
60_I	64_Q	0.678	1.00
49_P	179_L	0.669	1.00
41_R	189_Y	0.669	1.00
18_A	21_A	0.669	1.00
83_A	87_A	0.668	1.00
168_R	171_D	0.668	1.00
77_K	149_L	0.668	1.00
117_S	120_E	0.665	1.00
193_Y	231_Y	0.663	1.00
89_A	140_A	0.662	1.00
239_S	242_I	0.662	1.00
178_P	181_A	0.661	1.00
88_Q	91_L	0.661	1.00
24_W	28_Y	0.661	1.00
124_A	127_N	0.659	1.00
107_R	111_L	0.659	1.00
191_I	238_D	0.659	1.00
47_I	180_F	0.657	1.00
139_Q	142_L	0.654	1.00
25_L	29_Y	0.654	1.00
30_M	33_P	0.653	1.00
94_A	131_M	0.651	1.00
192_G	208_A	0.650	1.00
111_L	117_S	0.647	1.00
183_V	254_L	0.646	1.00
20_L	26_W	0.645	1.00
131_M	135_V	0.641	1.00
213_Y	259_P	0.641	1.00
189_Y	240_S	0.641	1.00
104_E	107_R	0.636	1.00
225_S	240_S	0.636	1.00
87_A	91_L	0.636	1.00
116_I	121_L	0.628	1.00
79_P	148_Q	0.625	1.00
204_E	224_S	0.625	1.00
39_K	235_V	0.624	1.00
150_A	155_R	0.623	1.00
129_K	133_A	0.622	1.00
84_E	87_A	0.620	1.00
94_A	98_L	0.617	1.00
150_A	153_E	0.615	1.00
205_G	222_H	0.612	1.00
20_L	23_W	0.612	1.00
24_W	27_N	0.612	1.00
120_E	124_A	0.611	1.00
118_A	125_N	0.610	1.00
48_T	178_P	0.609	1.00
89_A	92_A	0.609	1.00
49_P	52_S	0.606	1.00
21_A	26_W	0.606	1.00
118_A	121_L	0.603	1.00
148_Q	151_Q	0.602	1.00
12_I	16_V	0.599	1.00
114_N	117_S	0.598	1.00
43_E	169_I	0.598	1.00
191_I	242_I	0.597	1.00
208_A	241_L	0.594	1.00
14_V	17_V	0.594	1.00
36_R	262_F	0.591	1.00
193_Y	240_S	0.588	1.00
204_E	226_I	0.588	1.00
36_R	260_V	0.587	1.00
81_Q	84_E	0.585	1.00
167_T	171_D	0.583	1.00
240_S	244_D	0.583	1.00
16_V	20_L	0.582	1.00
119_E	122_D	0.581	1.00
58_L	165_L	0.580	1.00
83_A	145_A	0.580	1.00
36_R	198_K	0.579	1.00
97_D	127_N	0.575	1.00
210_I	258_V	0.574	1.00
230_I	237_S	0.569	1.00
171_D	177_K	0.568	1.00
202_I	223_V	0.564	1.00
92_A	96_S	0.562	1.00
84_E	145_A	0.561	1.00
48_T	177_K	0.557	1.00
107_R	119_E	0.557	1.00
131_M	134_S	0.557	1.00
96_S	100_K	0.556	1.00
215_D	219_L	0.553	1.00
141_T	145_A	0.552	1.00
235_V	238_D	0.551	1.00
78_T	81_Q	0.550	1.00
126_L	130_A	0.550	1.00
128_V	131_M	0.549	1.00
59_N	70_D	0.548	1.00
27_N	30_M	0.546	1.00
108_R	111_L	0.540	1.00
104_E	124_A	0.540	1.00
80_F	145_A	0.539	1.00
48_T	172_Y	0.539	1.00
19_V	26_W	0.537	1.00
187_S	242_I	0.536	1.00
86_N	144_Q	0.536	1.00
212_L	252_V	0.532	1.00
196_E	257_R	0.531	1.00
115_F	119_E	0.530	1.00
167_T	179_L	0.527	1.00
181_A	229_A	0.527	1.00
163_T	228_R	0.527	1.00
51_V	152_T	0.525	1.00
63_N	225_S	0.522	1.00
104_E	127_N	0.522	1.00
45_V	182_L	0.521	1.00
158_V	184_D	0.518	1.00
49_P	75_I	0.515	1.00
87_A	142_L	0.512	1.00
214_S	256_Q	0.511	1.00
167_T	177_K	0.510	1.00
78_T	150_A	0.510	1.00
28_Y	31_Q	0.509	1.00
42_A	183_V	0.507	1.00
205_G	223_V	0.504	1.00
82_I	85_L	0.502	1.00
164_N	178_P	0.500	1.00
228_R	253_R	0.500	1.00

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
2f1mA	2	0.807	100	0.312	Contact Map
3fppA	3	0.8667	100	0.332	Contact Map
4dk0A	5	0.9263	100	0.341	Contact Map
3lnnA	6	0.9439	100	0.342	Contact Map
4tkoB	1	0.8105	100	0.35	Contact Map
1vf7A	5	0.7825	100	0.377	Contact Map
3ne5B	3	0.8105	100	0.378	Contact Map
4l8jA	2	0.8947	100	0.384	Contact Map
4kkuA	1	0.6351	100	0.456	Contact Map
2k32A	1	0.4	99.8	0.644	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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