YDHJ - BACSU - GREMLIN Contacts

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YDHJ - Uncharacterized protein YdhJ

UniProt:	O05502	Sequences: MEISDIIYGQHHIDGVLEELIKSAPVQRLKGIYQGGASFLVNRKWNVTRYEHSIGVMLLIKKLGGTIEEQIAGLLHDVSHTAFSHVVDVVFENQAEDYHENIFQQVIVHSEIPDILQKHGYHTEELLSDDSRWTLLEQPAPELCADRTDYTLRDMYRYGHINLHEAQTFLDHLIVRNGRMFPDSIEAAEWFVSVYYKEVIDFFLNPVNVYGYEYLARALKAALRHDVISAEDLLKTDQEVLNILRASKNEEVLSLLTSIHPGIQVIEDDIQYDFHQKKKMRLIDPSIFLDDKWIKSSGVSEKVRKMGEAAYQKAKKGVYIKILKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (275)
Sequences:	1720 (1175)
Seq/√Len:	70.8

BACSU - YDHJ YWFO
HALSA - Q9HMK5 Q9HPP4 Q9HSK2
SULSO - Q97U95 Q7LXZ1 Q97XC0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_L	70_Q	4.243	1.00
61_K	70_Q	3.389	1.00
63_L	145_A	3.347	1.00
20_L	71_I	3.273	1.00
75_L	78_V	3.221	1.00
23_S	115_I	3.096	1.00
247_S	252_V	3.091	1.00
60_I	73_G	3.074	1.00
30_K	50_Y	3.069	1.00
218_A	256_L	3.046	1.00
258_S	263_I	2.946	1.00
151_T	198_E	2.840	1.00
27_Q	30_K	2.706	1.00
24_A	111_E	2.567	1.00
19_E	118_K	2.555	1.00
81_T	87_V	2.431	1.00
198_E	203_F	2.422	1.00
31_G	236_T	2.403	1.00
101_N	105_Q	2.341	1.00
59_L	145_A	2.311	1.00
245_R	260_H	2.223	1.00
112_I	116_L	2.165	1.00
6_I	44_K	2.141	1.00
173_L	182_P	2.117	1.00
113_P	117_Q	2.106	1.00
217_R	220_K	2.088	1.00
254_S	258_S	2.058	1.00
4_S	10_Q	2.010	1.00
9_G	167_Q	1.985	1.00
7_I	156_Y	1.980	1.00
17_L	57_M	1.964	1.00
249_N	252_V	1.942	1.00
56_V	73_G	1.916	1.00
38_S	208_N	1.915	1.00
57_M	70_Q	1.914	1.00
40_L	211_G	1.887	1.00
182_P	188_A	1.849	1.00
80_H	99_H	1.836	1.00
8_Y	152_L	1.829	1.00
22_K	30_K	1.825	1.00
77_D	146_D	1.815	1.00
214_Y	265_V	1.809	1.00
76_H	146_D	1.768	1.00
257_T	263_I	1.767	1.00
236_T	245_R	1.750	1.00
21_I	26_V	1.741	1.00
211_G	264_Q	1.729	1.00
168_T	205_N	1.709	1.00
47_V	154_D	1.693	1.00
262_G	266_I	1.688	1.00
56_V	145_A	1.670	1.00
257_T	261_P	1.642	0.99
111_E	116_L	1.637	0.99
6_I	156_Y	1.619	0.99
20_L	75_L	1.603	0.99
229_S	232_D	1.578	0.99
62_K	167_Q	1.562	0.99
3_I	43_R	1.483	0.99
46_N	51_E	1.477	0.99
112_I	115_I	1.450	0.99
66_T	170_L	1.443	0.99
158_Y	202_F	1.442	0.99
122_H	125_E	1.433	0.99
75_L	107_I	1.432	0.99
58_L	62_K	1.427	0.98
236_T	239_E	1.404	0.98
120_G	123_T	1.394	0.98
198_E	202_F	1.388	0.98
63_L	173_L	1.388	0.98
172_H	184_S	1.376	0.98
100_E	147_R	1.372	0.98
71_I	116_L	1.368	0.98
160_H	198_E	1.347	0.98
168_T	262_G	1.345	0.98
13_I	17_L	1.336	0.98
76_H	80_H	1.329	0.98
214_Y	264_Q	1.302	0.97
115_I	119_H	1.300	0.97
152_L	166_A	1.298	0.97
17_L	71_I	1.292	0.97
272_Y	276_Q	1.287	0.97
253_L	257_T	1.286	0.97
60_I	145_A	1.280	0.97
248_K	252_V	1.265	0.97
6_I	157_R	1.255	0.97
247_S	250_E	1.251	0.97
232_D	235_K	1.249	0.96
23_S	26_V	1.246	0.96
144_C	147_R	1.243	0.96
148_T	164_H	1.226	0.96
60_I	138_Q	1.225	0.96
131_S	136_L	1.221	0.96
14_D	17_L	1.216	0.96
13_I	18_E	1.215	0.96
100_E	150_Y	1.213	0.96
36_G	84_S	1.208	0.96
77_D	85_H	1.199	0.96
24_A	261_P	1.194	0.95
76_H	85_H	1.191	0.95
85_H	146_D	1.190	0.95
149_D	153_R	1.185	0.95
205_N	262_G	1.182	0.95
147_R	192_V	1.163	0.95
84_S	147_R	1.161	0.95
184_S	187_A	1.159	0.95
19_E	119_H	1.157	0.95
4_S	42_N	1.153	0.94
34_Q	154_D	1.118	0.94
100_E	103_F	1.114	0.93
161_I	198_E	1.101	0.93
258_S	265_V	1.100	0.93
97_D	102_I	1.097	0.93
43_R	47_V	1.093	0.93
245_R	248_K	1.085	0.92
151_T	194_V	1.083	0.92
111_E	114_D	1.082	0.92
38_S	42_N	1.079	0.92
111_E	115_I	1.078	0.92
39_F	48_T	1.072	0.92
27_Q	50_Y	1.072	0.92
51_E	157_R	1.072	0.92
62_K	65_G	1.067	0.92
81_T	233_L	1.066	0.92
49_R	55_G	1.059	0.92
88_D	193_S	1.054	0.91
31_G	261_P	1.036	0.91
12_H	171_D	1.035	0.91
35_G	158_Y	1.032	0.90
2_E	10_Q	1.027	0.90
86_V	212_Y	1.025	0.90
15_G	19_E	1.022	0.90
3_I	13_I	1.019	0.90
132_R	135_L	1.016	0.90
63_L	138_Q	1.006	0.89
193_S	197_K	1.006	0.89
22_K	262_G	1.003	0.89
18_E	22_K	1.002	0.89
129_D	136_L	0.997	0.89
149_D	154_D	0.994	0.89
50_Y	168_T	0.991	0.89
52_H	77_D	0.983	0.88
45_W	158_Y	0.982	0.88
31_G	238_Q	0.981	0.88
35_G	45_W	0.980	0.88
52_H	146_D	0.976	0.88
80_H	100_E	0.972	0.88
37_A	212_Y	0.972	0.88
13_I	57_M	0.964	0.87
219_L	240_V	0.964	0.87
80_H	84_S	0.964	0.87
117_Q	124_E	0.963	0.87
141_P	148_T	0.948	0.86
106_V	234_L	0.944	0.86
79_S	84_S	0.936	0.86
135_L	139_P	0.936	0.86
58_L	61_K	0.935	0.86
78_V	107_I	0.933	0.85
27_Q	83_F	0.924	0.85
59_L	63_L	0.916	0.84
239_E	245_R	0.910	0.84
199_V	204_L	0.907	0.84
147_R	191_F	0.897	0.83
80_H	85_H	0.894	0.83
20_L	112_I	0.894	0.83
76_H	99_H	0.891	0.83
85_H	100_E	0.886	0.82
117_Q	121_Y	0.885	0.82
41_V	102_I	0.884	0.82
114_D	117_Q	0.882	0.82
13_I	21_I	0.882	0.82
147_R	195_Y	0.877	0.82
88_D	144_C	0.874	0.81
3_I	7_I	0.872	0.81
130_D	133_W	0.870	0.81
116_L	120_G	0.869	0.81
35_G	151_T	0.866	0.81
22_K	205_N	0.865	0.81
27_Q	205_N	0.863	0.81
39_F	208_N	0.862	0.81
147_R	150_Y	0.854	0.80
271_Q	275_H	0.854	0.80
99_H	153_R	0.849	0.80
196_Y	200_I	0.847	0.79
161_I	196_Y	0.846	0.79
2_E	12_H	0.845	0.79
194_V	198_E	0.844	0.79
173_L	188_A	0.843	0.79
13_I	26_V	0.842	0.79
118_K	121_Y	0.840	0.79
244_L	248_K	0.839	0.79
76_H	100_E	0.831	0.78
248_K	261_P	0.831	0.78
52_H	76_H	0.821	0.77
236_T	240_V	0.820	0.77
50_Y	262_G	0.820	0.77
121_Y	124_E	0.816	0.77
44_K	157_R	0.811	0.76
37_A	215_L	0.808	0.76
100_E	146_D	0.808	0.76
35_G	38_S	0.804	0.76
116_L	121_Y	0.801	0.75
36_G	208_N	0.800	0.75
61_K	73_G	0.798	0.75
77_D	80_H	0.796	0.75
133_W	136_L	0.793	0.75
157_R	208_N	0.791	0.75
118_K	177_N	0.789	0.74
80_H	146_D	0.783	0.74
62_K	166_A	0.778	0.73
110_S	113_P	0.776	0.73
191_F	206_P	0.775	0.73
222_A	247_S	0.771	0.73
35_G	203_F	0.770	0.73
238_Q	241_L	0.767	0.72
151_T	203_F	0.765	0.72
210_Y	265_V	0.764	0.72
30_K	158_Y	0.762	0.72
8_Y	166_A	0.762	0.72
140_A	144_C	0.761	0.72
43_R	46_N	0.754	0.71
144_C	195_Y	0.753	0.71
121_Y	125_E	0.748	0.70
219_L	241_L	0.746	0.70
22_K	27_Q	0.746	0.70
66_T	166_A	0.744	0.70
142_E	147_R	0.743	0.70
174_I	181_F	0.742	0.70
55_G	153_R	0.741	0.70
4_S	196_Y	0.740	0.70
59_L	166_A	0.740	0.70
79_S	144_C	0.739	0.69
91_F	233_L	0.738	0.69
37_A	208_N	0.738	0.69
17_L	61_K	0.737	0.69
21_I	74_L	0.736	0.69
43_R	51_E	0.734	0.69
26_V	78_V	0.728	0.68
50_Y	205_N	0.720	0.67
268_D	272_Y	0.720	0.67
178_G	220_K	0.720	0.67
49_R	52_H	0.719	0.67
242_N	245_R	0.718	0.67
43_R	168_T	0.716	0.67
138_Q	192_V	0.714	0.67
151_T	202_F	0.714	0.67
165_E	187_A	0.713	0.67
208_N	212_Y	0.713	0.67
151_T	155_M	0.710	0.66
139_P	147_R	0.709	0.66
109_H	114_D	0.704	0.66
16_V	119_H	0.700	0.65
23_S	111_E	0.698	0.65
272_Y	275_H	0.698	0.65
150_Y	154_D	0.698	0.65
154_D	203_F	0.697	0.65
34_Q	100_E	0.696	0.65
87_V	142_E	0.695	0.65
2_E	171_D	0.694	0.65
6_I	10_Q	0.693	0.64
36_G	144_C	0.688	0.64
206_P	267_E	0.688	0.64
151_T	195_Y	0.687	0.64
130_D	134_T	0.684	0.63
73_G	139_P	0.684	0.63
159_G	165_E	0.678	0.63
106_V	230_A	0.675	0.62
57_M	61_K	0.674	0.62
5_D	8_Y	0.674	0.62
128_S	132_R	0.672	0.62
218_A	247_S	0.671	0.62
80_H	150_Y	0.669	0.62
28_R	49_R	0.665	0.61
29_L	53_S	0.665	0.61
26_V	75_L	0.660	0.61
22_K	266_I	0.659	0.61
81_T	91_F	0.659	0.61
101_N	248_K	0.658	0.60
218_A	259_I	0.656	0.60
93_N	220_K	0.656	0.60
235_K	249_N	0.652	0.60
77_D	100_E	0.652	0.60
88_D	189_E	0.651	0.60
151_T	162_N	0.651	0.60
220_K	275_H	0.646	0.59
239_E	242_N	0.641	0.58
78_V	103_F	0.640	0.58
214_Y	255_L	0.639	0.58
204_L	209_V	0.638	0.58
65_G	69_E	0.635	0.58
26_V	230_A	0.635	0.58
170_L	173_L	0.635	0.58
86_V	208_N	0.633	0.58
218_A	244_L	0.633	0.58
66_T	171_D	0.632	0.57
59_L	104_Q	0.631	0.57
223_L	226_D	0.630	0.57
51_E	168_T	0.627	0.57
13_I	167_Q	0.624	0.56
186_E	201_D	0.624	0.56
104_Q	107_I	0.624	0.56
155_M	160_H	0.623	0.56
53_S	116_L	0.622	0.56
240_V	245_R	0.620	0.56
79_S	103_F	0.618	0.56
129_D	134_T	0.618	0.56
115_I	118_K	0.617	0.56
99_H	154_D	0.615	0.55
19_E	22_K	0.614	0.55
79_S	82_A	0.612	0.55
16_V	19_E	0.608	0.55
8_Y	195_Y	0.608	0.55
35_G	79_S	0.606	0.54
141_P	144_C	0.605	0.54
228_I	231_E	0.604	0.54
145_A	169_F	0.604	0.54
195_Y	203_F	0.603	0.54
53_S	135_L	0.603	0.54
88_D	139_P	0.601	0.54
152_L	156_Y	0.601	0.54
22_K	50_Y	0.598	0.53
162_N	189_E	0.598	0.53
14_D	70_Q	0.596	0.53
180_M	271_Q	0.593	0.53
8_Y	11_H	0.592	0.53
65_G	68_E	0.590	0.52
128_S	235_K	0.589	0.52
26_V	73_G	0.588	0.52
78_V	112_I	0.587	0.52
122_H	127_L	0.587	0.52
28_R	84_S	0.587	0.52
270_I	274_F	0.586	0.52
186_E	196_Y	0.583	0.51
207_V	262_G	0.580	0.51
25_P	73_G	0.580	0.51
8_Y	94_Q	0.575	0.51
63_L	73_G	0.575	0.51
30_K	258_S	0.574	0.50
14_D	57_M	0.572	0.50
7_I	157_R	0.571	0.50
109_H	122_H	0.571	0.50
80_H	154_D	0.566	0.49
113_P	124_E	0.564	0.49
139_P	197_K	0.561	0.49
248_K	251_E	0.558	0.48
48_T	51_E	0.558	0.48
27_Q	168_T	0.556	0.48
190_W	197_K	0.556	0.48
79_S	99_H	0.556	0.48
141_P	184_S	0.554	0.48
169_F	202_F	0.551	0.48
247_S	253_L	0.550	0.47
118_K	231_E	0.547	0.47
30_K	40_L	0.546	0.47
107_I	237_D	0.545	0.47
6_I	11_H	0.544	0.47
67_I	82_A	0.543	0.47
114_D	118_K	0.542	0.46
47_V	198_E	0.541	0.46
229_S	254_S	0.541	0.46
79_S	199_V	0.540	0.46
160_H	194_V	0.540	0.46
148_T	191_F	0.540	0.46
57_M	206_P	0.540	0.46
92_E	102_I	0.539	0.46
19_E	39_F	0.538	0.46
99_H	146_D	0.537	0.46
114_D	248_K	0.536	0.46
138_Q	141_P	0.536	0.46
183_D	267_E	0.536	0.46
34_Q	150_Y	0.535	0.46
38_S	66_T	0.534	0.46
58_L	129_D	0.534	0.46
11_H	14_D	0.533	0.45
197_K	201_D	0.533	0.45
15_G	71_I	0.532	0.45
211_G	218_A	0.530	0.45
6_I	159_G	0.530	0.45
64_G	69_E	0.529	0.45
41_V	92_E	0.528	0.45
36_G	86_V	0.527	0.45
61_K	228_I	0.524	0.44
70_Q	241_L	0.523	0.44
228_I	233_L	0.522	0.44
19_E	120_G	0.520	0.44
20_L	46_N	0.519	0.44
144_C	150_Y	0.519	0.44
90_V	209_V	0.519	0.44
168_T	207_V	0.519	0.44
85_H	99_H	0.519	0.44
218_A	264_Q	0.517	0.43
155_M	194_V	0.516	0.43
7_I	175_V	0.515	0.43
158_Y	192_V	0.515	0.43
6_I	204_L	0.515	0.43
195_Y	199_V	0.514	0.43
213_E	216_A	0.514	0.43
138_Q	145_A	0.513	0.43
88_D	162_N	0.513	0.43
27_Q	262_G	0.512	0.43
57_M	148_T	0.511	0.43
37_A	88_D	0.510	0.43
34_Q	80_H	0.508	0.42
40_L	242_N	0.508	0.42
8_Y	30_K	0.508	0.42
60_I	64_G	0.507	0.42
45_W	214_Y	0.504	0.42
26_V	53_S	0.502	0.42
208_N	211_G	0.502	0.42
123_T	126_L	0.501	0.42
214_Y	218_A	0.500	0.41
147_R	151_T	0.500	0.41
70_Q	73_G	0.500	0.41

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
4lrlA	4	0.9877	100	0.281	Contact Map
4mz7A	4	0.9631	100	0.288	Contact Map
2hekA	4	0.9415	100	0.314	Contact Map
2q14A	4	0.96	100	0.335	Contact Map
3bg2A	4	0.7908	100	0.697	Contact Map
2pgsA	4	0.8	100	0.703	Contact Map
4x9eA	4	0.9354	99.9	0.719	Contact Map
2dqbA	4	0.7969	99.9	0.726	Contact Map
4n6wA	1	0.4985	98.3	0.895	Contact Map
3gw7A	2	0.5631	97.6	0.911	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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