YVJA - BACSU - GREMLIN Contacts

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YVJA - UPF0750 membrane protein YvjA

UniProt:	O34792	Sequences: MDVRNKTLWILRDYVYILIGAAITAVSFNVFLLPNKIAAGGVSGISTILQSYGFEAAYVQWIINIPLFIAGVILLGGKFGLKTLAGSVFLPLVVFLTRDIQPATHHELLAAIFGGVGIGIGIGIVYLGKGSTGGTALAAQIIHKYSGLSLGKCLAIIDGMIVVTAMIVFNIEQGLYAMLGVYVSSKTIDVVQVGFNRSKMALIITKQEQAVKEAVLQKIDRGVTKISAVGGYTDDDRPILMCVVGQTEFTKLKQIVKQIDESAFVIVADASEVLGEGFKRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	281 (271)
Sequences:	3735 (2696)
Seq/√Len:	163.8

BACSU - YVJA YQFU YDEO YXKD YPJC 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
18_L	85_A	5.797	1.00
207_Q	210_A	5.147	1.00
227_S	236_D	3.967	1.00
228_A	239_I	3.845	1.00
213_E	217_Q	3.484	1.00
206_K	237_R	3.420	1.00
205_T	211_V	3.399	1.00
22_A	93_V	3.026	1.00
201_A	252_L	2.781	1.00
113_F	175_L	2.743	1.00
42_V	63_I	2.596	1.00
229_V	234_D	2.546	1.00
214_A	255_I	2.454	1.00
226_I	239_I	2.431	1.00
229_V	238_P	2.384	1.00
205_T	208_E	2.356	1.00
214_A	218_K	2.288	1.00
49_L	52_Y	2.272	1.00
209_Q	213_E	2.265	1.00
227_S	238_P	2.124	1.00
199_K	269_D	2.103	1.00
223_V	231_G	2.051	1.00
13_D	82_K	2.002	1.00
14_Y	85_A	2.001	1.00
88_V	92_L	1.954	1.00
29_N	97_T	1.946	1.00
18_L	89_F	1.943	1.00
25_A	93_V	1.935	1.00
20_G	121_G	1.907	1.00
26_V	30_V	1.904	1.00
24_T	90_L	1.903	1.00
221_R	248_E	1.893	1.00
166_M	174_G	1.885	1.00
27_S	118_I	1.860	1.00
186_K	190_V	1.849	1.00
16_Y	128_G	1.840	1.00
57_A	95_F	1.799	1.00
166_M	171_I	1.779	1.00
125_V	132_T	1.751	1.00
212_K	231_G	1.742	1.00
49_L	59_V	1.734	1.00
106_H	176_Y	1.723	1.00
151_G	189_D	1.697	1.00
35_N	110_A	1.687	1.00
223_V	240_L	1.681	1.00
225_K	240_L	1.662	1.00
256_V	263_A	1.660	1.00
215_V	252_L	1.606	1.00
256_V	265_V	1.598	1.00
208_E	238_P	1.579	1.00
69_I	73_I	1.566	1.00
206_K	235_D	1.538	1.00
219_I	252_L	1.538	1.00
13_D	128_G	1.529	1.00
229_V	236_D	1.519	1.00
214_A	259_I	1.509	1.00
209_Q	234_D	1.503	1.00
170_N	173_Q	1.500	1.00
108_L	179_L	1.493	1.00
212_K	234_D	1.489	1.00
123_G	191_V	1.467	1.00
200_M	268_A	1.446	1.00
206_K	262_S	1.434	1.00
241_M	266_I	1.415	1.00
160_M	164_T	1.403	1.00
212_K	225_K	1.393	1.00
202_L	241_M	1.386	1.00
26_V	97_T	1.375	1.00
45_I	49_L	1.368	1.00
17_I	86_G	1.366	1.00
65_I	69_I	1.364	1.00
79_F	131_S	1.346	1.00
156_I	160_M	1.334	1.00
20_G	125_V	1.306	1.00
210_A	259_I	1.294	1.00
244_V	252_L	1.294	1.00
162_V	181_V	1.291	1.00
228_A	237_R	1.285	1.00
42_V	67_L	1.283	1.00
203_I	256_V	1.282	1.00
262_S	276_E	1.278	1.00
215_V	242_C	1.274	1.00
60_Q	94_V	1.270	1.00
57_A	91_P	1.269	1.00
32_L	114_G	1.269	1.00
22_A	97_T	1.266	1.00
119_G	123_G	1.257	1.00
55_E	95_F	1.254	1.00
155_A	185_S	1.232	1.00
27_S	117_G	1.224	1.00
75_L	79_F	1.206	1.00
253_K	272_E	1.195	1.00
81_L	85_A	1.190	1.00
27_S	121_G	1.187	1.00
36_K	173_Q	1.185	1.00
21_A	89_F	1.182	1.00
202_L	268_A	1.179	1.00
17_I	130_G	1.178	1.00
139_A	154_L	1.173	1.00
72_V	77_G	1.163	1.00
159_G	163_V	1.150	1.00
182_Y	186_K	1.145	1.00
61_W	91_P	1.141	1.00
200_M	266_I	1.141	1.00
71_G	80_G	1.138	1.00
107_E	173_Q	1.133	1.00
249_F	267_V	1.130	1.00
33_L	56_A	1.127	1.00
111_A	115_G	1.125	1.00
214_A	258_Q	1.124	1.00
216_L	231_G	1.124	1.00
225_K	238_P	1.122	1.00
200_M	270_A	1.116	1.00
29_N	98_R	1.116	1.00
14_Y	82_K	1.106	1.00
11_L	15_V	1.106	1.00
72_V	80_G	1.100	1.00
68_F	87_S	1.095	1.00
12_R	16_Y	1.082	1.00
15_V	19_I	1.078	0.99
116_V	187_T	1.078	0.99
201_A	249_F	1.078	0.99
45_I	164_T	1.074	0.99
54_F	59_V	1.074	0.99
109_L	113_F	1.071	0.99
260_D	263_A	1.065	0.99
224_T	228_A	1.065	0.99
212_K	223_V	1.050	0.99
89_F	93_V	1.049	0.99
57_A	61_W	1.032	0.99
225_K	231_G	1.028	0.99
215_V	221_R	1.023	0.99
14_Y	18_L	1.022	0.99
255_I	258_Q	1.015	0.99
230_G	233_T	1.011	0.99
85_A	89_F	0.995	0.99
75_L	140_Q	0.987	0.99
86_G	130_G	0.979	0.99
199_K	272_E	0.973	0.99
47_T	50_Q	0.967	0.99
38_A	165_A	0.964	0.99
31_F	113_F	0.960	0.99
10_I	13_D	0.955	0.99
106_H	172_E	0.953	0.99
266_I	270_A	0.952	0.99
38_A	158_D	0.947	0.99
111_A	179_L	0.947	0.99
202_L	226_I	0.946	0.99
36_K	51_S	0.934	0.99
58_Y	95_F	0.931	0.99
59_V	63_I	0.930	0.99
16_Y	124_I	0.921	0.98
142_I	146_S	0.920	0.98
74_L	141_I	0.916	0.98
252_L	256_V	0.916	0.98
216_L	223_V	0.915	0.98
43_S	94_V	0.911	0.98
200_M	241_M	0.910	0.98
74_L	145_Y	0.907	0.98
250_T	254_Q	0.900	0.98
107_E	111_A	0.898	0.98
32_L	180_G	0.894	0.98
189_D	246_Q	0.891	0.98
200_M	243_V	0.889	0.98
66_P	69_I	0.884	0.98
202_L	266_I	0.873	0.98
211_V	255_I	0.869	0.98
131_S	140_Q	0.868	0.98
70_A	74_L	0.861	0.98
68_F	83_T	0.859	0.97
45_I	48_I	0.857	0.97
21_A	86_G	0.855	0.97
151_G	188_I	0.854	0.97
151_G	185_S	0.849	0.97
115_G	119_G	0.844	0.97
58_Y	62_I	0.844	0.97
120_I	191_V	0.842	0.97
184_S	188_I	0.840	0.97
75_L	131_S	0.838	0.97
148_L	153_C	0.837	0.97
198_S	242_C	0.834	0.97
78_K	82_K	0.833	0.97
225_K	229_V	0.833	0.97
116_V	182_Y	0.832	0.97
214_A	217_Q	0.829	0.97
38_A	177_A	0.823	0.97
11_L	14_Y	0.822	0.97
122_I	126_Y	0.820	0.97
216_L	222_G	0.819	0.97
50_Q	56_A	0.817	0.97
10_I	82_K	0.812	0.96
243_V	266_I	0.812	0.96
21_A	125_V	0.808	0.96
245_G	248_E	0.806	0.96
201_A	244_V	0.801	0.96
255_I	259_I	0.798	0.96
122_I	188_I	0.797	0.96
126_Y	140_Q	0.797	0.96
205_T	260_D	0.795	0.96
201_A	256_V	0.793	0.96
226_I	241_M	0.793	0.96
213_E	234_D	0.791	0.96
48_I	169_F	0.787	0.96
154_L	158_D	0.786	0.96
24_T	121_G	0.786	0.96
23_I	120_I	0.785	0.96
253_K	274_L	0.780	0.96
112_I	183_V	0.779	0.96
37_I	111_A	0.773	0.95
22_A	89_F	0.772	0.95
81_L	84_L	0.769	0.95
107_E	110_A	0.767	0.95
109_L	175_L	0.763	0.95
156_I	159_G	0.760	0.95
149_S	189_D	0.755	0.95
61_W	88_V	0.754	0.95
68_F	84_L	0.753	0.95
12_R	128_G	0.748	0.94
48_I	164_T	0.747	0.94
132_T	136_A	0.747	0.94
93_V	96_L	0.746	0.94
21_A	90_L	0.745	0.94
27_S	31_F	0.742	0.94
186_K	189_D	0.742	0.94
142_I	153_C	0.741	0.94
68_F	71_G	0.738	0.94
212_K	216_L	0.736	0.94
61_W	65_I	0.734	0.94
218_K	251_K	0.729	0.94
181_V	185_S	0.725	0.93
254_Q	258_Q	0.722	0.93
62_I	66_P	0.718	0.93
95_F	98_R	0.717	0.93
123_G	127_L	0.717	0.93
218_K	255_I	0.715	0.93
67_L	138_A	0.714	0.93
138_A	142_I	0.710	0.93
207_Q	259_I	0.709	0.93
222_G	232_Y	0.708	0.93
112_I	179_L	0.705	0.93
223_V	242_C	0.704	0.92
46_S	60_Q	0.703	0.92
55_E	58_Y	0.701	0.92
208_E	211_V	0.696	0.92
141_I	145_Y	0.696	0.92
24_T	118_I	0.694	0.92
67_L	83_T	0.686	0.91
257_K	274_L	0.686	0.91
164_T	167_I	0.686	0.91
71_G	79_F	0.685	0.91
135_T	157_I	0.685	0.91
221_R	245_G	0.683	0.91
207_Q	260_D	0.683	0.91
110_A	172_E	0.682	0.91
45_I	63_I	0.679	0.91
66_P	70_A	0.679	0.91
44_G	176_Y	0.677	0.91
152_K	189_D	0.676	0.91
160_M	163_V	0.676	0.91
149_S	152_K	0.675	0.91
155_A	182_Y	0.675	0.91
118_I	184_S	0.674	0.91
199_K	267_V	0.673	0.91
140_Q	150_L	0.669	0.90
125_V	130_G	0.667	0.90
135_T	169_F	0.666	0.90
28_F	90_L	0.662	0.90
49_L	63_I	0.661	0.90
52_Y	59_V	0.661	0.90
209_Q	238_P	0.658	0.90
211_V	259_I	0.657	0.90
30_V	101_Q	0.655	0.90
25_A	90_L	0.655	0.90
28_F	33_L	0.652	0.89
162_V	165_A	0.650	0.89
79_F	140_Q	0.650	0.89
135_T	158_D	0.648	0.89
224_T	230_G	0.646	0.89
126_Y	136_A	0.645	0.89
111_A	183_V	0.641	0.88
154_L	188_I	0.641	0.88
16_Y	19_I	0.640	0.88
19_I	23_I	0.640	0.88
87_S	91_P	0.637	0.88
122_I	132_T	0.636	0.88
23_I	117_G	0.633	0.88
106_H	111_A	0.631	0.88
197_R	246_Q	0.631	0.88
122_I	184_S	0.628	0.87
218_K	258_Q	0.624	0.87
251_K	254_Q	0.624	0.87
158_D	177_A	0.624	0.87
230_G	237_R	0.622	0.87
30_V	97_T	0.621	0.87
28_F	46_S	0.621	0.87
221_R	277_G	0.620	0.87
70_A	141_I	0.619	0.87
254_Q	257_K	0.619	0.87
33_L	47_T	0.619	0.87
158_D	277_G	0.619	0.87
201_A	267_V	0.618	0.87
59_V	62_I	0.618	0.87
82_K	129_K	0.617	0.87
203_I	252_L	0.616	0.86
195_F	198_S	0.616	0.86
113_F	178_M	0.613	0.86
104_T	172_E	0.610	0.86
124_I	128_G	0.610	0.86
46_S	241_M	0.608	0.86
204_I	241_M	0.606	0.86
69_I	72_V	0.604	0.85
111_A	180_G	0.604	0.85
208_E	212_K	0.602	0.85
37_I	104_T	0.601	0.85
137_L	151_G	0.600	0.85
105_H	172_E	0.598	0.85
86_G	132_T	0.598	0.85
38_A	47_T	0.598	0.85
83_T	137_L	0.596	0.85
115_G	183_V	0.593	0.84
49_L	54_F	0.593	0.84
193_V	271_S	0.591	0.84
146_S	153_C	0.590	0.84
33_L	50_Q	0.590	0.84
243_V	270_A	0.587	0.84
133_G	136_A	0.586	0.84
43_S	90_L	0.584	0.83
56_A	60_Q	0.581	0.83
107_E	172_E	0.579	0.83
221_R	278_F	0.578	0.83
50_Q	59_V	0.577	0.83
152_K	155_A	0.577	0.83
46_S	63_I	0.576	0.83
177_A	244_V	0.576	0.83
165_A	174_G	0.576	0.83
267_V	272_E	0.574	0.82
68_F	106_H	0.573	0.82
30_V	34_P	0.572	0.82
199_K	237_R	0.572	0.82
203_I	242_C	0.570	0.82
104_T	110_A	0.569	0.82
92_L	96_L	0.566	0.82
107_E	176_Y	0.566	0.82
47_T	51_S	0.565	0.81
253_K	257_K	0.564	0.81
24_T	122_I	0.564	0.81
83_T	87_S	0.564	0.81
39_A	136_A	0.563	0.81
150_L	189_D	0.562	0.81
82_K	177_A	0.561	0.81
73_I	91_P	0.556	0.80
140_Q	144_K	0.556	0.80
244_V	249_F	0.554	0.80
157_I	161_I	0.551	0.80
264_F	273_V	0.550	0.80
174_G	180_G	0.549	0.80
47_T	241_M	0.549	0.80
170_N	174_G	0.549	0.80
68_F	138_A	0.547	0.79
51_S	169_F	0.547	0.79
84_L	87_S	0.543	0.79
224_T	264_F	0.538	0.78
163_V	167_I	0.538	0.78
50_Q	53_G	0.536	0.78
156_I	164_T	0.536	0.78
77_G	80_G	0.535	0.78
169_F	173_Q	0.535	0.78
12_R	258_Q	0.533	0.78
126_Y	192_Q	0.531	0.77
119_G	188_I	0.531	0.77
143_H	146_S	0.529	0.77
211_V	256_V	0.527	0.77
202_L	239_I	0.526	0.77
225_K	234_D	0.526	0.77
12_R	127_L	0.525	0.76
109_L	182_Y	0.523	0.76
76_G	198_S	0.522	0.76
220_D	276_E	0.521	0.76
101_Q	104_T	0.521	0.76
34_P	127_L	0.520	0.76
70_A	73_I	0.519	0.76
22_A	26_V	0.518	0.76
202_L	270_A	0.517	0.75
120_I	187_T	0.516	0.75
46_S	56_A	0.516	0.75
37_I	107_E	0.516	0.75
196_N	201_A	0.515	0.75
118_I	126_Y	0.513	0.75
126_Y	139_A	0.512	0.75
37_I	114_G	0.511	0.75
164_T	178_M	0.511	0.75
166_M	170_N	0.510	0.74
28_F	43_S	0.510	0.74
68_F	137_L	0.508	0.74
47_T	56_A	0.508	0.74
115_G	184_S	0.507	0.74
18_L	93_V	0.506	0.74
108_L	118_I	0.504	0.74
66_P	186_K	0.504	0.74
140_Q	158_D	0.503	0.73
137_L	188_I	0.502	0.73
205_T	238_P	0.502	0.73
148_L	152_K	0.502	0.73
233_T	262_S	0.502	0.73
29_N	99_D	0.500	0.73
232_Y	264_F	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	0.2598	99.9	0.69	Contact Map
4rwwA	3	0.2989	80	0.943	Contact Map
4affA	3	0.306	79.1	0.944	Contact Map
2dclA	5	0.3167	78	0.944	Contact Map
2eg2A	5	0.2918	76.8	0.945	Contact Map
3ncqA	4	0.306	76.5	0.945	Contact Map
3t9zA	3	0.2989	76.1	0.945	Contact Map
4co3A	3	0.3025	75.9	0.945	Contact Map
2gw8A	3	0.3025	75.3	0.946	Contact Map
4r25A	3	0.3132	74.8	0.946	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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