YDHB - BACSU - GREMLIN Contacts

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YDHB - UPF0721 transmembrane protein YdhB

UniProt:	O05493	Sequences: MLIILVMFLLGIILGFIGAGGAGFVIALLTLLFHIPIHTALGTSLAGMAFTSLSGAYSHYREGNIQMKIGLIVGGFAAVGSFFGAKLTSFIPADLLHYLTAGMLFLSAILILIRLFILKEKAQVNQSTLSTYTRAVILGIAAGVLSGTFGIGSAPFIQIGLMIMLNLSIRHSVGTTMLVIIPLAVGGGIGYITEGFVDYVLLVKVLVGTMCGAYVGAKFTNLMPKVVLKSAIFLTPAIAGLLLLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	245 (234)
Sequences:	9701 (6664)
Seq/√Len:	435.6

ECOLI - YFCA
BACSU - YDHB YJNA YUNE YRKJ YTNM
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
12_I	219_F	3.681	1.00
80_G	140_I	3.670	1.00
87_L	144_V	3.153	1.00
66_Q	171_H	2.919	1.00
4_I	208_G	2.696	1.00
226_V	230_S	2.548	1.00
54_S	210_M	2.528	1.00
60_Y	67_M	2.517	1.00
6_V	28_L	2.471	1.00
227_V	230_S	2.452	1.00
74_G	182_P	2.435	1.00
109_I	113_I	2.417	1.00
50_F	206_L	2.348	1.00
45_L	187_G	2.337	1.00
76_F	136_V	2.287	1.00
70_G	178_L	2.225	1.00
218_K	222_L	2.224	1.00
168_S	171_H	2.189	1.00
54_S	214_Y	2.182	1.00
108_A	240_G	2.074	1.00
82_F	190_G	2.037	1.00
39_T	42_G	1.983	1.00
69_I	167_L	1.957	1.00
43_T	202_L	1.928	1.00
101_A	240_G	1.916	1.00
46_A	202_L	1.876	1.00
224_P	227_V	1.828	1.00
66_Q	69_I	1.824	1.00
108_A	237_A	1.822	1.00
59_H	64_N	1.791	1.00
58_S	217_A	1.749	1.00
8_F	211_C	1.748	1.00
7_M	205_V	1.737	1.00
10_L	24_F	1.723	1.00
29_L	205_V	1.715	1.00
102_G	106_L	1.711	1.00
68_K	71_L	1.673	1.00
105_F	240_G	1.666	1.00
138_L	160_G	1.665	1.00
108_A	233_F	1.635	1.00
112_L	233_F	1.630	1.00
8_F	212_G	1.627	1.00
140_I	144_V	1.597	1.00
59_H	220_T	1.577	1.00
71_L	75_G	1.568	1.00
237_A	241_L	1.562	1.00
86_K	90_F	1.524	1.00
12_I	215_V	1.520	1.00
198_D	201_L	1.518	1.00
62_E	221_N	1.511	1.00
68_K	72_I	1.510	1.00
192_I	199_Y	1.497	1.00
70_G	175_T	1.492	1.00
5_L	9_L	1.465	1.00
53_L	181_I	1.438	1.00
116_F	119_K	1.432	1.00
95_L	99_L	1.416	1.00
83_F	140_I	1.411	1.00
56_A	178_L	1.409	1.00
78_A	186_G	1.405	1.00
230_S	234_L	1.388	1.00
71_L	74_G	1.379	1.00
203_V	207_V	1.368	1.00
189_I	193_T	1.366	1.00
81_S	187_G	1.365	1.00
80_G	84_G	1.355	1.00
64_N	221_N	1.339	1.00
30_T	37_I	1.337	1.00
200_V	204_K	1.336	1.00
4_I	204_K	1.334	1.00
207_V	211_C	1.332	1.00
214_Y	218_K	1.327	1.00
103_M	149_F	1.323	1.00
49_A	185_V	1.315	1.00
35_I	201_L	1.306	1.00
39_T	198_D	1.300	1.00
57_Y	61_R	1.299	1.00
67_M	71_L	1.297	1.00
55_G	177_M	1.286	1.00
133_T	137_I	1.276	1.00
101_A	105_F	1.270	1.00
77_A	183_L	1.256	1.00
135_A	165_L	1.239	1.00
82_F	86_K	1.238	1.00
212_G	216_G	1.219	1.00
36_P	39_T	1.204	1.00
7_M	208_G	1.199	1.00
159_I	162_M	1.197	1.00
64_N	174_G	1.195	1.00
91_I	148_T	1.194	1.00
111_I	232_I	1.172	1.00
234_L	238_I	1.172	1.00
67_M	70_G	1.171	1.00
116_F	120_E	1.168	1.00
76_F	80_G	1.167	1.00
56_A	60_Y	1.167	1.00
41_L	191_Y	1.165	1.00
196_F	200_V	1.148	1.00
208_G	212_G	1.147	1.00
113_I	116_F	1.145	1.00
42_G	197_V	1.143	1.00
212_G	215_V	1.137	1.00
59_H	217_A	1.129	1.00
55_G	213_A	1.114	1.00
17_I	231_A	1.102	1.00
4_I	207_V	1.100	1.00
80_G	144_V	1.097	1.00
85_A	187_G	1.088	1.00
131_T	134_R	1.080	1.00
85_A	190_G	1.078	1.00
190_G	194_E	1.075	1.00
56_A	181_I	1.071	1.00
76_F	139_G	1.068	1.00
53_L	57_Y	1.060	1.00
180_I	183_L	1.055	1.00
56_A	67_M	1.032	1.00
44_S	48_M	1.029	1.00
133_T	136_V	1.027	1.00
59_H	174_G	1.023	1.00
153_S	157_I	1.022	1.00
227_V	231_A	1.011	1.00
170_R	220_T	1.010	1.00
83_F	86_K	0.991	1.00
162_M	172_S	0.986	1.00
137_I	141_A	0.983	1.00
4_I	8_F	0.982	1.00
94_D	98_Y	0.977	1.00
51_T	209_T	0.974	1.00
26_I	44_S	0.965	1.00
25_V	205_V	0.963	1.00
156_F	159_I	0.963	1.00
160_G	164_M	0.960	1.00
58_S	62_E	0.955	1.00
65_I	175_T	0.955	1.00
22_A	147_G	0.955	1.00
77_A	179_V	0.948	1.00
73_V	179_V	0.946	1.00
34_H	40_A	0.944	1.00
60_Y	65_I	0.935	1.00
58_S	214_Y	0.924	1.00
218_K	221_N	0.916	1.00
98_Y	102_G	0.915	1.00
75_G	79_V	0.906	1.00
169_I	173_V	0.905	1.00
84_G	144_V	0.904	1.00
10_L	25_V	0.903	1.00
43_T	197_V	0.901	1.00
95_L	98_Y	0.895	1.00
3_I	204_K	0.891	1.00
54_S	213_A	0.889	1.00
114_R	229_K	0.878	1.00
211_C	214_Y	0.878	1.00
156_F	160_G	0.876	1.00
49_A	188_G	0.873	1.00
8_F	208_G	0.871	1.00
109_I	237_A	0.871	1.00
238_I	241_L	0.870	1.00
159_I	163_I	0.864	1.00
83_F	144_V	0.856	1.00
203_V	206_L	0.856	1.00
150_G	153_S	0.851	1.00
232_I	236_P	0.849	1.00
105_F	237_A	0.843	1.00
93_A	97_H	0.843	1.00
204_K	208_G	0.841	1.00
134_R	137_I	0.841	1.00
58_S	218_K	0.834	1.00
223_M	227_V	0.827	1.00
3_I	201_L	0.827	1.00
86_K	89_S	0.825	1.00
83_F	87_L	0.803	1.00
114_R	117_I	0.800	1.00
76_F	79_V	0.797	1.00
106_L	110_L	0.796	1.00
11_G	21_G	0.793	1.00
146_S	153_S	0.792	1.00
15_G	55_G	0.789	1.00
54_S	58_S	0.788	1.00
92_P	95_L	0.787	1.00
105_F	109_I	0.783	1.00
39_T	43_T	0.783	1.00
70_G	179_V	0.782	1.00
88_T	191_Y	0.781	1.00
213_A	217_A	0.779	1.00
14_L	22_A	0.779	1.00
30_T	40_A	0.777	1.00
3_I	205_V	0.774	1.00
162_M	169_I	0.774	1.00
191_Y	196_F	0.771	1.00
128_T	131_T	0.770	1.00
10_L	28_L	0.769	1.00
42_G	188_G	0.769	1.00
146_S	183_L	0.768	1.00
62_E	218_K	0.767	1.00
87_L	90_F	0.766	1.00
142_A	153_S	0.766	1.00
94_D	97_H	0.758	1.00
65_I	70_G	0.756	1.00
139_G	143_G	0.755	1.00
142_A	157_I	0.753	1.00
52_S	150_G	0.752	1.00
14_L	24_F	0.750	1.00
50_F	210_M	0.746	1.00
16_F	216_G	0.746	1.00
108_A	236_P	0.738	1.00
35_I	39_T	0.737	1.00
177_M	180_I	0.736	1.00
220_T	228_L	0.734	1.00
178_L	182_P	0.729	1.00
79_V	83_F	0.727	1.00
52_S	180_I	0.726	1.00
67_M	178_L	0.726	1.00
7_M	11_G	0.724	1.00
14_L	146_S	0.724	1.00
60_Y	63_G	0.723	1.00
22_A	48_M	0.721	1.00
15_G	217_A	0.719	1.00
169_I	232_I	0.718	1.00
153_S	159_I	0.717	1.00
8_F	215_V	0.715	1.00
25_V	29_L	0.715	1.00
99_L	149_F	0.714	1.00
158_Q	173_V	0.713	1.00
224_P	228_L	0.712	1.00
47_G	209_T	0.708	1.00
12_I	212_G	0.704	1.00
57_Y	60_Y	0.703	1.00
98_Y	101_A	0.700	1.00
150_G	176_T	0.698	1.00
81_S	85_A	0.698	1.00
238_I	242_L	0.696	1.00
85_A	191_Y	0.693	1.00
45_L	150_G	0.691	1.00
200_V	203_V	0.691	1.00
158_Q	172_S	0.690	1.00
16_F	228_L	0.690	1.00
37_I	41_L	0.682	1.00
137_I	140_I	0.678	1.00
72_I	132_Y	0.678	1.00
73_V	139_G	0.677	1.00
46_A	188_G	0.673	1.00
85_A	186_G	0.670	1.00
58_S	61_R	0.670	1.00
41_L	45_L	0.669	1.00
89_S	194_E	0.668	1.00
38_H	96_L	0.666	1.00
202_L	206_L	0.662	1.00
7_M	25_V	0.662	1.00
215_V	218_K	0.658	1.00
23_G	104_L	0.658	1.00
100_T	149_F	0.657	1.00
86_K	190_G	0.652	0.99
45_L	146_S	0.650	0.99
72_I	75_G	0.650	0.99
43_T	198_D	0.649	0.99
77_A	157_I	0.647	0.99
35_I	198_D	0.643	0.99
146_S	151_I	0.642	0.99
48_M	153_S	0.642	0.99
45_L	48_M	0.641	0.99
188_G	202_L	0.638	0.99
38_H	42_G	0.636	0.99
64_N	171_H	0.634	0.99
127_S	131_T	0.632	0.99
188_G	192_I	0.631	0.99
166_N	172_S	0.622	0.99
153_S	180_I	0.619	0.99
197_V	202_L	0.618	0.99
210_M	214_Y	0.616	0.99
7_M	201_L	0.613	0.99
48_M	52_S	0.613	0.99
91_I	95_L	0.613	0.99
154_A	213_A	0.613	0.99
108_A	112_L	0.612	0.99
171_H	174_G	0.611	0.99
66_Q	71_L	0.611	0.99
4_I	7_M	0.611	0.99
172_S	176_T	0.610	0.99
48_M	146_S	0.610	0.99
52_S	181_I	0.610	0.99
16_F	219_F	0.608	0.99
8_F	12_I	0.604	0.99
159_I	172_S	0.599	0.99
176_T	180_I	0.597	0.99
68_K	132_Y	0.595	0.99
53_L	56_A	0.593	0.99
154_A	176_T	0.591	0.99
41_L	88_T	0.591	0.99
158_Q	179_V	0.586	0.99
38_H	88_T	0.583	0.99
129_L	132_Y	0.580	0.99
31_L	242_L	0.578	0.99
106_L	109_I	0.578	0.99
16_F	223_M	0.572	0.99
14_L	51_T	0.572	0.99
25_V	44_S	0.572	0.99
233_F	237_A	0.571	0.99
37_I	97_H	0.571	0.99
100_T	243_L	0.571	0.99
105_F	241_L	0.570	0.99
86_K	194_E	0.567	0.99
13_I	24_F	0.566	0.99
142_A	156_F	0.566	0.99
48_M	184_A	0.560	0.98
112_L	230_S	0.557	0.98
93_A	148_T	0.555	0.98
26_I	100_T	0.555	0.98
4_I	211_C	0.554	0.98
192_I	197_V	0.552	0.98
82_F	193_T	0.551	0.98
12_I	16_F	0.549	0.98
132_Y	136_V	0.549	0.98
21_G	151_I	0.548	0.98
219_F	223_M	0.545	0.98
79_V	140_I	0.543	0.98
87_L	91_I	0.543	0.98
129_L	133_T	0.543	0.98
17_I	235_T	0.543	0.98
81_S	186_G	0.541	0.98
41_L	96_L	0.541	0.98
48_M	180_I	0.536	0.98
153_S	176_T	0.535	0.98
219_F	222_L	0.535	0.98
139_G	157_I	0.534	0.98
8_F	11_G	0.533	0.98
11_G	209_T	0.533	0.98
170_R	225_K	0.532	0.98
226_V	229_K	0.528	0.98
17_I	213_A	0.527	0.98
111_I	233_F	0.523	0.98
14_L	180_I	0.521	0.98
230_S	233_F	0.520	0.97
46_A	206_L	0.520	0.97
11_G	15_G	0.519	0.97
157_I	179_V	0.519	0.97
24_F	27_A	0.519	0.97
38_H	41_L	0.518	0.97
23_G	149_F	0.516	0.97
126_Q	131_T	0.513	0.97
37_I	96_L	0.513	0.97
211_C	215_V	0.513	0.97
74_G	77_A	0.512	0.97
46_A	199_Y	0.509	0.97
26_I	40_A	0.507	0.97
52_S	184_A	0.506	0.97
23_G	156_F	0.504	0.97
35_I	43_T	0.504	0.97
73_V	161_L	0.504	0.97
156_F	161_L	0.502	0.97
66_Q	175_T	0.501	0.97
69_I	171_H	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	0.8653	85.3	0.895	Contact Map
2gfpA	2	0.8449	82.7	0.899	Contact Map
1pw4A	1	0.8408	80.5	0.901	Contact Map
3wdoA	1	0.8531	75	0.906	Contact Map
2cfqA	1	0.8531	74.7	0.906	Contact Map
4j05A	3	0.8408	61.6	0.914	Contact Map
4pypA	1	0.7837	53.8	0.918	Contact Map
4m64A	1	0.8612	44.5	0.922	Contact Map
4zw9A	1	0.8449	40.5	0.924	Contact Map
4xnjA	1	0.9633	38.7	0.925	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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