YPJC - BACSU - GREMLIN Contacts

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YPJC - UPF0750 membrane protein YpjC

UniProt:	P42978	Sequences: MLGEIRLKNIFFILIGAAIFSFGLVHFNMQNNLAEGGFTGITLLLYALFHISPSISNLVLNIPIFFIGWRLLGRTMFVYTLVGTVALSLFLSIFQRYEIHMPLQHDLALAALFAGVFIGAGLGIIFKFGGTTGGVDIIARLVNKYFGIPMGRTMFAFDACVIILSLLTYLSYKEAMYTLVAVFVAARLIDFIQEGGYAAKGATIISSKNDLIQKKILEEMERGVTILKGQGSYTKEDIDVLYCVVPKNELVMLKSVINSIDPHAFVAVSDVHDVLGEGFTLDENKNPLPR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (272)
Sequences:	3718 (2690)
Seq/√Len:	163.1

BACSU - YPJC YXKD YDEO YQFU YVJA YITT YITE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_L	82_V	5.766	1.00
208_K	211_L	5.100	1.00
228_K	237_D	3.937	1.00
229_G	240_V	3.816	1.00
214_K	218_E	3.498	1.00
207_S	238_I	3.366	1.00
206_S	212_I	3.161	1.00
18_A	90_F	2.985	1.00
113_F	176_M	2.736	1.00
202_A	253_L	2.710	1.00
230_Q	235_K	2.546	1.00
38_F	60_L	2.539	1.00
230_Q	239_D	2.407	1.00
215_K	256_V	2.366	1.00
206_S	209_N	2.358	1.00
227_L	240_V	2.342	1.00
210_D	214_K	2.285	1.00
215_K	219_E	2.214	1.00
200_K	270_D	2.142	1.00
228_K	239_D	2.110	1.00
224_V	232_S	2.074	1.00
45_L	49_F	2.040	1.00
10_I	82_V	2.019	1.00
9_N	79_Y	1.994	1.00
85_V	89_L	1.968	1.00
25_V	94_F	1.966	1.00
14_L	86_A	1.941	1.00
166_L	175_A	1.916	1.00
16_G	121_G	1.913	1.00
222_R	249_E	1.907	1.00
23_G	118_I	1.884	1.00
20_F	87_L	1.874	1.00
21_S	90_F	1.866	1.00
187_R	191_F	1.855	1.00
22_F	26_H	1.849	1.00
12_F	128_F	1.846	1.00
54_S	92_S	1.799	1.00
125_I	132_T	1.747	1.00
213_Q	232_S	1.733	1.00
151_G	190_D	1.710	1.00
166_L	172_Y	1.702	1.00
257_I	264_A	1.684	1.00
106_D	177_Y	1.683	1.00
45_L	56_S	1.673	1.00
216_I	253_L	1.669	1.00
226_I	241_L	1.657	1.00
207_S	236_E	1.656	1.00
224_V	241_L	1.628	1.00
31_N	110_A	1.614	1.00
257_I	266_V	1.581	1.00
171_S	174_E	1.568	1.00
209_N	239_D	1.568	1.00
9_N	128_F	1.558	1.00
66_F	70_R	1.532	1.00
220_M	253_L	1.524	1.00
123_G	192_I	1.501	1.00
213_Q	235_K	1.498	1.00
207_S	263_H	1.487	1.00
230_Q	237_D	1.486	1.00
215_K	260_I	1.481	1.00
210_D	235_K	1.479	1.00
108_A	180_V	1.465	1.00
242_Y	267_A	1.444	1.00
201_G	269_S	1.426	1.00
76_M	131_T	1.417	1.00
213_Q	226_I	1.410	1.00
18_A	94_F	1.410	1.00
22_F	94_F	1.388	1.00
203_T	242_Y	1.377	1.00
25_V	95_Q	1.376	1.00
160_C	164_L	1.365	1.00
13_I	83_G	1.364	1.00
16_G	125_I	1.362	1.00
156_A	160_C	1.361	1.00
38_F	64_I	1.324	1.00
41_I	45_L	1.318	1.00
229_G	238_I	1.315	1.00
245_V	253_L	1.306	1.00
62_I	66_F	1.299	1.00
57_N	91_L	1.274	1.00
52_S	92_S	1.273	1.00
54_S	88_S	1.271	1.00
162_I	182_V	1.269	1.00
263_H	277_E	1.265	1.00
211_L	260_I	1.264	1.00
28_N	114_A	1.257	1.00
119_G	123_G	1.243	1.00
216_I	243_C	1.237	1.00
155_F	186_A	1.222	1.00
72_L	76_M	1.220	1.00
78_V	82_V	1.198	1.00
68_G	77_F	1.194	1.00
13_I	130_G	1.185	1.00
139_A	154_M	1.182	1.00
204_I	257_I	1.177	1.00
17_A	86_A	1.177	1.00
201_G	267_A	1.167	1.00
32_N	174_E	1.166	1.00
23_G	121_G	1.162	1.00
183_F	187_R	1.161	1.00
69_W	74_R	1.153	1.00
226_I	239_D	1.153	1.00
23_G	117_F	1.142	1.00
203_T	269_S	1.142	1.00
65_F	84_T	1.141	1.00
254_K	273_D	1.139	1.00
201_G	271_V	1.132	1.00
7_L	11_F	1.123	1.00
217_L	232_S	1.123	1.00
159_A	163_I	1.123	1.00
116_V	188_L	1.119	1.00
10_I	79_Y	1.117	1.00
58_L	88_S	1.115	1.00
215_K	259_S	1.112	1.00
142_V	146_F	1.112	1.00
250_L	268_V	1.108	1.00
29_M	53_P	1.105	1.00
54_S	58_L	1.099	1.00
107_L	174_E	1.090	1.00
261_D	264_A	1.085	1.00
225_T	229_G	1.081	0.99
202_A	250_L	1.075	0.99
111_A	115_G	1.071	0.99
86_A	90_F	1.067	0.99
231_G	234_T	1.059	0.99
8_K	12_F	1.059	0.99
10_I	14_L	1.049	0.99
69_W	77_F	1.049	0.99
11_F	15_I	1.044	0.99
82_V	86_A	1.042	0.99
106_D	173_K	1.033	0.99
213_Q	224_V	1.033	0.99
109_L	113_F	1.032	0.99
256_V	259_S	1.032	0.99
226_I	232_S	1.027	0.99
71_L	145_Y	1.026	0.99
41_I	164_L	1.024	0.99
51_I	56_S	1.023	0.99
43_L	46_Y	0.997	0.99
34_A	165_S	0.983	0.99
72_L	140_R	0.978	0.99
27_F	113_F	0.976	0.99
83_G	130_G	0.975	0.99
216_I	222_R	0.970	0.99
203_T	227_L	0.970	0.99
55_I	92_S	0.963	0.99
200_K	273_D	0.957	0.99
267_A	271_V	0.952	0.99
111_A	180_V	0.938	0.99
56_S	60_L	0.928	0.98
34_A	158_D	0.925	0.98
12_F	124_I	0.924	0.98
201_G	244_V	0.923	0.98
151_G	186_A	0.914	0.98
190_D	247_K	0.912	0.98
28_N	181_A	0.911	0.98
107_L	111_A	0.911	0.98
151_G	189_I	0.909	0.98
253_L	257_I	0.907	0.98
201_G	242_Y	0.901	0.98
212_I	256_V	0.898	0.98
116_V	183_F	0.898	0.98
17_A	83_G	0.896	0.98
203_T	267_A	0.895	0.98
32_N	47_A	0.894	0.98
251_V	255_S	0.893	0.98
217_L	224_V	0.892	0.98
39_T	91_L	0.891	0.98
63_P	66_F	0.885	0.98
75_T	79_Y	0.879	0.98
6_R	9_N	0.868	0.98
72_L	131_T	0.868	0.98
71_L	141_L	0.865	0.98
115_G	119_G	0.863	0.98
92_S	95_Q	0.845	0.97
246_P	249_E	0.844	0.97
122_L	126_F	0.840	0.97
67_I	71_L	0.839	0.97
217_L	223_G	0.837	0.97
34_A	178_T	0.830	0.97
227_L	242_Y	0.828	0.97
17_A	125_I	0.824	0.97
44_L	48_L	0.823	0.97
226_I	230_Q	0.823	0.97
148_I	153_T	0.823	0.97
120_A	192_I	0.819	0.97
131_T	140_R	0.819	0.97
65_F	80_T	0.817	0.97
202_A	245_V	0.813	0.96
185_A	189_I	0.812	0.96
215_K	218_E	0.806	0.96
20_F	121_G	0.805	0.96
33_L	111_A	0.798	0.96
46_Y	53_P	0.798	0.96
202_A	257_I	0.792	0.96
154_M	158_D	0.790	0.96
107_L	110_A	0.790	0.96
65_F	81_L	0.790	0.96
199_A	243_C	0.789	0.96
41_I	44_L	0.787	0.96
256_V	260_I	0.786	0.96
244_V	267_A	0.785	0.96
8_K	128_F	0.782	0.96
122_L	189_I	0.778	0.95
123_G	127_K	0.774	0.95
55_I	59_V	0.773	0.95
141_L	145_Y	0.772	0.95
19_I	120_A	0.771	0.95
126_F	140_R	0.770	0.95
214_K	235_K	0.770	0.95
109_L	176_M	0.769	0.95
23_G	27_F	0.769	0.95
46_Y	50_H	0.764	0.95
44_L	169_Y	0.764	0.95
64_I	138_I	0.763	0.95
142_V	153_T	0.758	0.95
44_L	164_L	0.758	0.95
156_A	159_A	0.757	0.95
59_V	63_P	0.757	0.95
18_A	86_A	0.755	0.95
63_P	67_I	0.755	0.95
213_Q	217_L	0.750	0.94
255_S	259_S	0.748	0.94
132_T	136_D	0.735	0.94
149_P	152_R	0.734	0.94
6_R	79_Y	0.734	0.94
45_L	51_I	0.734	0.94
208_K	260_I	0.731	0.94
149_P	190_D	0.731	0.94
17_A	87_L	0.731	0.94
78_V	81_L	0.730	0.94
24_L	87_L	0.729	0.94
112_L	184_V	0.726	0.93
135_V	157_F	0.724	0.93
254_K	275_L	0.722	0.93
200_K	268_V	0.722	0.93
58_L	62_I	0.718	0.93
58_L	85_V	0.718	0.93
52_S	55_I	0.718	0.93
187_R	190_D	0.717	0.93
65_F	68_G	0.712	0.93
138_I	142_V	0.709	0.93
104_Q	173_K	0.708	0.93
206_S	261_D	0.707	0.93
224_V	243_C	0.704	0.92
182_V	186_A	0.703	0.92
41_I	60_L	0.703	0.92
209_N	212_I	0.702	0.92
135_V	169_Y	0.701	0.92
110_A	173_K	0.699	0.92
7_L	10_I	0.699	0.92
219_E	252_M	0.698	0.92
112_L	180_V	0.698	0.92
164_L	167_L	0.696	0.92
219_E	256_V	0.696	0.92
26_H	94_F	0.693	0.92
155_F	183_F	0.692	0.92
160_C	163_I	0.689	0.92
222_R	246_P	0.685	0.91
45_L	60_L	0.685	0.91
90_F	93_I	0.681	0.91
208_K	261_D	0.676	0.91
24_L	42_T	0.675	0.91
42_T	57_N	0.674	0.91
64_I	80_T	0.673	0.91
198_A	247_K	0.673	0.91
210_D	239_D	0.673	0.91
20_F	118_I	0.672	0.91
66_F	69_W	0.671	0.90
258_N	275_L	0.670	0.90
40_G	177_Y	0.669	0.90
118_I	185_A	0.669	0.90
252_M	255_S	0.669	0.90
140_R	150_M	0.668	0.90
15_I	19_I	0.667	0.90
79_Y	129_G	0.666	0.90
24_L	29_M	0.665	0.90
12_F	15_I	0.664	0.90
205_I	242_Y	0.664	0.90
133_G	136_D	0.663	0.90
152_R	190_D	0.662	0.90
49_F	56_S	0.662	0.90
222_R	278_G	0.661	0.90
94_F	97_Y	0.658	0.90
225_T	231_G	0.655	0.89
125_I	130_G	0.655	0.89
212_I	260_I	0.655	0.89
19_I	117_F	0.653	0.89
223_G	233_Y	0.651	0.89
202_A	268_V	0.651	0.89
68_G	76_M	0.649	0.89
135_V	158_D	0.649	0.89
122_L	132_T	0.649	0.89
124_I	128_F	0.648	0.89
106_D	111_A	0.640	0.88
255_S	258_N	0.638	0.88
76_M	140_R	0.637	0.88
126_F	136_D	0.636	0.88
105_H	173_K	0.635	0.88
84_T	88_S	0.635	0.88
111_A	184_V	0.632	0.88
222_R	279_F	0.631	0.88
231_G	238_I	0.629	0.87
154_M	189_I	0.625	0.87
163_I	167_L	0.624	0.87
162_I	165_S	0.622	0.87
29_M	46_Y	0.622	0.87
140_R	144_K	0.622	0.87
21_S	87_L	0.618	0.87
56_S	59_V	0.617	0.86
29_M	43_L	0.617	0.86
137_I	151_G	0.616	0.86
122_L	185_A	0.615	0.86
165_S	175_A	0.614	0.86
111_A	181_A	0.614	0.86
102_P	108_A	0.612	0.86
244_V	271_V	0.610	0.86
113_F	179_L	0.608	0.86
39_T	87_L	0.607	0.86
67_I	141_L	0.607	0.86
204_I	253_L	0.605	0.85
73_G	199_A	0.601	0.85
152_R	155_F	0.601	0.85
80_T	137_I	0.600	0.85
35_E	136_D	0.599	0.85
175_A	181_A	0.599	0.85
209_N	213_Q	0.596	0.85
194_E	272_H	0.596	0.85
89_L	93_I	0.595	0.84
34_A	43_L	0.594	0.84
158_D	178_T	0.591	0.84
219_E	259_S	0.591	0.84
268_V	273_D	0.587	0.84
200_K	238_I	0.587	0.84
8_K	127_K	0.587	0.84
46_Y	56_S	0.582	0.83
203_T	240_V	0.579	0.83
42_T	242_Y	0.579	0.83
265_F	274_V	0.578	0.83
115_G	184_V	0.576	0.82
119_G	189_I	0.576	0.82
104_Q	110_A	0.573	0.82
178_T	245_V	0.572	0.82
67_I	70_R	0.572	0.82
245_V	250_L	0.572	0.82
81_L	84_T	0.571	0.82
206_S	239_D	0.570	0.82
79_Y	178_T	0.568	0.82
48_L	63_P	0.567	0.81
158_D	278_G	0.566	0.81
150_M	190_D	0.566	0.81
120_A	188_L	0.565	0.81
204_I	243_C	0.563	0.81
70_R	88_S	0.562	0.81
83_G	132_T	0.562	0.81
26_H	30_Q	0.556	0.80
137_I	189_I	0.553	0.80
254_K	258_N	0.553	0.80
20_F	122_L	0.549	0.79
43_L	242_Y	0.546	0.79
225_T	265_F	0.545	0.79
107_L	177_Y	0.542	0.79
18_A	22_F	0.541	0.78
42_T	60_L	0.541	0.78
43_L	53_P	0.540	0.78
50_H	56_S	0.540	0.78
53_P	57_N	0.538	0.78
203_T	271_V	0.535	0.78
126_F	150_M	0.535	0.78
157_F	161_V	0.532	0.77
221_E	277_E	0.527	0.77
43_L	47_A	0.527	0.77
148_I	152_R	0.523	0.76
44_L	161_V	0.523	0.76
212_I	257_I	0.522	0.76
234_T	263_H	0.521	0.76
52_S	96_R	0.521	0.76
226_I	235_K	0.521	0.76
103_L	107_L	0.521	0.76
104_Q	107_L	0.520	0.76
112_L	238_I	0.519	0.76
143_N	147_G	0.517	0.75
211_L	214_K	0.516	0.75
115_G	185_A	0.515	0.75
109_L	183_F	0.515	0.75
65_F	106_D	0.514	0.75
63_P	187_R	0.514	0.75
30_Q	127_K	0.512	0.75
65_F	138_I	0.511	0.74
196_G	199_A	0.510	0.74
64_I	133_G	0.510	0.74
74_R	77_F	0.509	0.74
54_S	57_N	0.508	0.74
156_A	164_L	0.508	0.74
207_S	212_I	0.508	0.74
262_P	270_D	0.507	0.74
98_E	103_L	0.505	0.74
86_A	93_I	0.504	0.73
218_E	221_E	0.503	0.73
171_S	175_A	0.503	0.73
47_A	169_Y	0.503	0.73
9_N	75_T	0.503	0.73
108_A	118_I	0.502	0.73
241_L	266_V	0.502	0.73
9_N	12_F	0.501	0.73
166_L	171_S	0.501	0.73
80_T	84_T	0.500	0.73
28_N	165_S	0.500	0.73

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
3hluA	2	0.2517	99.9	0.691	Contact Map
2gw8A	3	0.3103	81	0.943	Contact Map
3l7pA	4	0.2862	76.4	0.946	Contact Map
4rwwA	3	0.2897	76.2	0.946	Contact Map
2dclA	5	0.3	75.6	0.946	Contact Map
2eg2A	5	0.3	74.5	0.946	Contact Map
4co3A	3	0.2966	73.8	0.947	Contact Map
4affA	3	0.3207	71.5	0.948	Contact Map
3ncqA	4	0.3207	71.1	0.948	Contact Map
2j9cA	3	0.3276	70.8	0.948	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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