YRKJ - BACSU - GREMLIN Contacts

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YRKJ - UPF0721 transmembrane protein YrkJ

UniProt:	P54437	Sequences: MDIAFITTLFIIGFIGAFISGMIGIGGAVINYPMLLYIPSLVGVMSLTAHEVSGIGAIQVFFATLGGVWAYRKSGLINKTLIIYMGSSILLGSVLGSYFSHYISEKGINFIYGILAIIAVILMFIPKKGQKGQEHSEDKEVIFNKWLASSLAFIIGGVSGILGAGGAFILVPIMLSILNIPVRVTVASSLAITFLSSIGATVGKVITGQVLFVPALVLMITSLIASPIGASVGQKVNTKFLQWVLAQLIGATAIKIWLELL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	261 (242)
Sequences:	9685 (6698)
Seq/√Len:	430.6

ECOLI - YFCA
BACSU - YRKJ YUNE YDHB YTNM YJNA
HALSA - O54662
SULSO - Q981D0 Q97WF4 Q97UT0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_G	153_F	3.789	1.00
18_F	232_V	3.686	1.00
99_F	157_G	3.037	1.00
78_N	184_V	2.952	1.00
10_F	221_T	2.732	1.00
72_R	79_K	2.548	1.00
239_K	243_W	2.546	1.00
66_G	223_L	2.425	1.00
151_L	173_I	2.379	1.00
62_F	219_M	2.366	1.00
12_I	34_M	2.346	1.00
86_G	195_L	2.324	1.00
240_F	243_W	2.306	1.00
121_I	125_I	2.256	1.00
231_S	235_K	2.254	1.00
66_G	227_P	2.198	1.00
88_S	149_S	2.191	1.00
57_A	200_A	2.168	1.00
82_I	191_A	2.164	1.00
181_P	184_V	2.117	1.00
94_V	203_G	2.048	1.00
113_G	253_A	2.023	1.00
120_V	253_A	1.993	1.00
254_I	258_L	1.921	1.00
55_I	215_A	1.916	1.00
51_E	54_G	1.912	1.00
81_L	180_I	1.894	1.00
237_N	240_F	1.857	1.00
78_N	81_L	1.805	1.00
71_Y	76_L	1.786	1.00
58_I	215_A	1.783	1.00
14_F	224_I	1.758	1.00
120_V	250_G	1.744	1.00
80_T	83_I	1.743	1.00
16_G	30_I	1.734	1.00
70_A	230_A	1.716	1.00
13_G	218_L	1.711	1.00
14_F	225_A	1.681	1.00
35_L	218_L	1.675	1.00
6_I	217_V	1.662	1.00
117_I	253_A	1.627	1.00
155_I	169_I	1.601	1.00
124_F	246_A	1.588	1.00
98_Y	102_Y	1.576	1.00
18_F	228_I	1.568	1.00
71_Y	233_G	1.565	1.00
83_I	87_S	1.550	1.00
90_L	199_G	1.547	1.00
80_T	84_Y	1.536	1.00
153_F	157_G	1.532	1.00
211_L	214_P	1.524	1.00
120_V	246_A	1.520	1.00
250_G	254_I	1.510	1.00
74_S	234_Q	1.469	1.00
83_I	86_G	1.467	1.00
216_L	220_I	1.462	1.00
82_I	188_S	1.461	1.00
11_I	15_I	1.436	1.00
107_G	111_I	1.429	1.00
243_W	247_Q	1.417	1.00
114_I	118_I	1.405	1.00
68_V	191_A	1.387	1.00
202_V	206_I	1.385	1.00
227_P	231_S	1.375	1.00
13_G	221_T	1.373	1.00
128_K	131_K	1.361	1.00
205_V	212_F	1.360	1.00
92_G	96_G	1.350	1.00
220_I	224_I	1.347	1.00
95_L	153_F	1.345	1.00
67_G	190_L	1.344	1.00
61_F	198_I	1.335	1.00
113_G	257_W	1.321	1.00
170_L	192_I	1.309	1.00
213_V	217_V	1.309	1.00
115_L	162_L	1.306	1.00
76_L	187_A	1.305	1.00
76_L	234_Q	1.300	1.00
7_T	11_I	1.297	1.00
247_Q	251_A	1.296	1.00
65_L	194_F	1.295	1.00
69_W	73_K	1.279	1.00
51_E	211_L	1.272	1.00
94_V	98_Y	1.266	1.00
68_V	72_R	1.258	1.00
88_S	152_A	1.250	1.00
225_A	229_G	1.247	1.00
146_W	150_S	1.242	1.00
36_L	49_A	1.240	1.00
93_S	200_A	1.235	1.00
79_K	83_I	1.229	1.00
79_K	82_I	1.216	1.00
171_V	185_T	1.212	1.00
10_F	217_V	1.199	1.00
89_I	196_S	1.198	1.00
48_T	51_E	1.198	1.00
113_G	117_I	1.196	1.00
88_S	92_G	1.165	1.00
203_G	207_T	1.158	1.00
97_S	203_G	1.156	1.00
103_I	161_I	1.154	1.00
65_L	69_W	1.153	1.00
193_T	196_S	1.150	1.00
67_G	226_S	1.144	1.00
71_Y	230_A	1.142	1.00
92_G	157_G	1.127	1.00
123_M	245_L	1.111	1.00
183_R	233_G	1.109	1.00
125_I	128_K	1.108	1.00
148_A	178_L	1.108	1.00
175_L	185_T	1.105	1.00
10_F	220_I	1.104	1.00
221_T	225_A	1.101	1.00
53_S	204_K	1.100	1.00
225_A	228_I	1.076	1.00
87_S	91_L	1.066	1.00
209_Q	213_V	1.054	1.00
47_L	214_P	1.054	1.00
68_V	79_K	1.051	1.00
146_W	149_S	1.043	1.00
85_M	174_M	1.031	1.00
164_A	168_F	1.027	1.00
144_N	147_L	1.013	1.00
150_S	154_I	1.010	1.00
175_L	182_V	0.989	1.00
70_A	227_P	0.989	1.00
31_N	218_L	0.988	1.00
128_K	132_G	0.986	1.00
95_L	98_Y	0.983	1.00
54_G	210_V	0.980	1.00
68_V	194_F	0.975	1.00
23_I	244_V	0.972	1.00
10_F	14_F	0.971	1.00
71_Y	187_A	0.969	1.00
233_G	241_L	0.966	1.00
166_G	170_L	0.960	1.00
171_V	189_S	0.956	1.00
63_A	222_S	0.955	1.00
106_K	110_F	0.954	1.00
89_I	192_I	0.950	1.00
9_L	214_P	0.949	1.00
182_V	186_V	0.946	1.00
56_G	60_V	0.942	1.00
110_F	114_I	0.942	1.00
8_T	11_I	0.941	1.00
9_L	217_V	0.938	1.00
97_S	200_A	0.936	1.00
240_F	244_V	0.933	1.00
66_G	226_S	0.925	1.00
231_S	234_Q	0.921	1.00
85_M	192_I	0.920	1.00
216_L	219_M	0.919	1.00
72_R	77_I	0.907	1.00
251_A	254_I	0.900	1.00
95_L	157_G	0.899	1.00
28_A	160_G	0.897	1.00
77_I	188_S	0.897	1.00
152_A	170_L	0.890	1.00
74_S	231_S	0.887	1.00
51_E	55_I	0.884	1.00
70_A	74_S	0.883	1.00
61_F	201_T	0.879	1.00
9_L	218_L	0.879	1.00
107_G	110_F	0.876	1.00
72_R	75_G	0.875	1.00
121_I	250_G	0.862	1.00
36_L	52_V	0.861	1.00
255_K	258_L	0.861	1.00
171_V	186_V	0.860	1.00
166_G	172_P	0.860	1.00
118_I	122_L	0.854	1.00
21_G	230_A	0.843	1.00
32_Y	56_G	0.841	1.00
16_G	31_N	0.841	1.00
224_I	227_P	0.837	1.00
117_I	121_I	0.836	1.00
55_I	210_V	0.828	1.00
226_S	230_A	0.827	1.00
147_L	150_S	0.827	1.00
91_L	95_L	0.826	1.00
98_Y	101_H	0.824	1.00
126_P	129_G	0.819	1.00
217_V	221_T	0.815	1.00
96_G	157_G	0.812	1.00
97_S	199_G	0.811	1.00
117_I	250_G	0.810	1.00
126_P	242_Q	0.809	1.00
14_F	221_T	0.805	1.00
77_I	82_I	0.804	1.00
191_A	195_L	0.800	1.00
14_F	228_I	0.798	1.00
64_T	163_G	0.796	1.00
70_A	73_K	0.792	1.00
31_N	35_L	0.791	1.00
55_I	211_L	0.791	1.00
70_A	231_S	0.790	1.00
170_L	174_M	0.790	1.00
22_M	229_G	0.789	1.00
251_A	255_K	0.787	1.00
21_G	67_G	0.784	1.00
245_L	249_I	0.782	1.00
173_I	177_I	0.779	1.00
66_G	70_A	0.773	1.00
159_S	196_S	0.769	1.00
99_F	102_Y	0.762	1.00
64_T	193_T	0.757	1.00
236_V	240_F	0.751	1.00
29_V	116_A	0.745	1.00
14_F	18_F	0.742	1.00
47_L	51_E	0.742	1.00
155_I	166_G	0.741	1.00
20_S	28_A	0.735	1.00
100_S	204_K	0.732	1.00
159_S	166_G	0.732	1.00
95_L	99_F	0.730	1.00
89_I	170_L	0.728	1.00
20_S	159_S	0.727	1.00
60_V	166_G	0.723	1.00
253_A	257_W	0.722	1.00
79_K	191_A	0.720	1.00
54_G	201_T	0.716	1.00
184_V	187_A	0.716	1.00
84_Y	145_K	0.714	1.00
213_V	216_L	0.712	1.00
62_F	223_L	0.710	1.00
105_E	109_N	0.709	1.00
59_Q	222_S	0.708	1.00
47_L	211_L	0.706	1.00
106_K	109_N	0.701	1.00
49_A	53_S	0.699	1.00
88_S	91_L	0.697	1.00
17_A	27_G	0.697	1.00
93_S	97_S	0.696	1.00
117_I	257_W	0.696	1.00
50_H	108_I	0.695	1.00
20_S	25_I	0.694	1.00
57_A	163_G	0.694	1.00
166_G	193_T	0.691	1.00
110_F	113_G	0.690	1.00
13_G	31_N	0.689	1.00
20_S	30_I	0.689	1.00
204_K	209_Q	0.688	1.00
13_G	17_A	0.687	1.00
28_A	60_V	0.685	1.00
8_T	12_I	0.681	1.00
104_S	107_G	0.681	1.00
101_H	207_T	0.671	1.00
10_F	13_G	0.668	1.00
142_I	146_W	0.668	1.00
84_Y	87_S	0.666	1.00
163_G	189_S	0.666	1.00
53_S	100_S	0.665	1.00
98_Y	207_T	0.664	1.00
97_S	204_K	0.663	1.00
223_L	227_P	0.663	1.00
82_I	192_I	0.662	1.00
60_V	197_S	0.662	1.00
163_G	166_G	0.661	1.00
246_A	250_G	0.660	1.00
38_I	47_L	0.660	1.00
22_M	241_L	0.658	0.99
58_I	201_T	0.656	0.99
201_T	215_A	0.656	0.99
228_I	231_S	0.655	0.99
16_G	34_M	0.654	0.99
18_F	225_A	0.652	0.99
50_H	54_G	0.651	0.99
190_L	193_T	0.651	0.99
120_V	124_F	0.649	0.99
150_S	153_F	0.648	0.99
159_S	164_A	0.644	0.99
119_A	168_F	0.642	0.99
105_E	161_I	0.641	0.99
13_G	214_P	0.633	0.99
98_Y	203_G	0.632	0.99
210_V	215_A	0.631	0.99
19_I	30_I	0.630	0.99
85_M	152_A	0.629	0.99
169_I	172_P	0.627	0.99
155_I	170_L	0.625	0.99
64_T	194_F	0.623	0.99
182_V	245_L	0.623	0.99
22_M	236_V	0.623	0.99
103_I	107_G	0.617	0.99
166_G	189_S	0.617	0.99
201_T	205_V	0.615	0.99
39_P	52_V	0.612	0.99
20_S	63_A	0.605	0.99
60_V	64_T	0.605	0.99
180_I	184_V	0.604	0.99
142_I	145_K	0.602	0.99
111_I	162_L	0.602	0.99
215_A	219_M	0.597	0.99
232_V	236_V	0.597	0.99
99_F	103_I	0.593	0.99
37_Y	256_I	0.592	0.99
185_T	189_S	0.592	0.99
60_V	159_S	0.587	0.99
183_R	238_T	0.585	0.99
36_L	39_P	0.583	0.99
10_F	224_I	0.582	0.99
23_I	248_L	0.581	0.99
65_L	68_V	0.580	0.99
69_W	72_R	0.578	0.99
91_L	153_F	0.576	0.99
189_S	193_T	0.573	0.99
20_S	193_T	0.572	0.99
80_T	145_K	0.572	0.99
53_S	57_A	0.569	0.99
147_L	173_I	0.569	0.99
17_A	222_S	0.569	0.99
58_I	219_M	0.569	0.99
57_A	60_V	0.569	0.99
14_F	17_A	0.568	0.99
212_F	216_L	0.568	0.99
120_V	249_I	0.563	0.98
205_V	210_V	0.562	0.98
123_M	246_A	0.562	0.98
78_N	83_I	0.556	0.98
84_Y	149_S	0.555	0.98
22_M	232_V	0.553	0.98
237_N	241_L	0.552	0.98
197_S	200_A	0.552	0.98
23_I	226_S	0.546	0.98
232_V	235_K	0.545	0.98
222_S	226_S	0.543	0.98
50_H	53_S	0.543	0.98
124_F	243_W	0.540	0.98
76_L	184_V	0.534	0.98
29_V	162_L	0.534	0.98
53_S	108_I	0.533	0.98
152_A	156_G	0.531	0.98
31_N	56_G	0.527	0.98
60_V	193_T	0.526	0.98
114_I	257_W	0.526	0.98
112_Y	256_I	0.525	0.98
117_I	254_I	0.523	0.97
60_V	245_L	0.519	0.97
20_S	60_V	0.517	0.97
99_F	161_I	0.517	0.97
149_S	152_A	0.515	0.97
58_I	212_F	0.515	0.97
21_G	226_S	0.514	0.97
84_Y	88_S	0.513	0.97
37_Y	255_K	0.513	0.97
130_Q	133_Q	0.513	0.97
63_A	163_G	0.513	0.97
32_Y	52_V	0.510	0.97
228_I	232_V	0.509	0.97
125_I	129_G	0.508	0.97
49_A	108_I	0.505	0.97
13_G	55_I	0.505	0.97
34_M	38_I	0.505	0.97
18_F	22_M	0.505	0.97
116_A	249_I	0.505	0.97
101_H	209_Q	0.504	0.97
31_N	60_V	0.503	0.97
238_T	242_Q	0.502	0.97
26_G	33_P	0.502	0.97
30_I	33_P	0.502	0.97
39_P	218_L	0.500	0.97
47_L	52_V	0.500	0.97
148_A	174_M	0.500	0.97

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
3o7qA	1	0.8659	82.9	0.906	Contact Map
1pw4A	1	0.8391	77.8	0.911	Contact Map
4rp9A	2	0.4789	72.6	0.915	Contact Map
2gfpA	2	0.8391	69.8	0.916	Contact Map
4j05A	3	0.751	64.8	0.919	Contact Map
2cfqA	1	0.8391	55.2	0.924	Contact Map
3wdoA	1	0.8467	43.5	0.929	Contact Map
4m64A	1	0.8429	40.4	0.93	Contact Map
4pypA	1	0.8276	35.6	0.932	Contact Map
4zw9A	1	0.7893	30.3	0.934	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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