YYDH - BACSU - GREMLIN Contacts

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YYDH - Putative peptide zinc metalloprotease protein YydH

UniProt:	Q45594	Sequences: MKILKYEDEKYEVLVQNNVFIKDKKSGEYYKNSLNSLSDKQLLRFKMYKEKVSPKFFYLFLSFTALMFILNYIHLIKLQNGLSSVFYGWKMWIIIVIYFIMNIVLHELGHIYSLKFFGKNFDKVGFKLNFYVFPAFYVQLNETYMLSRNEKIIVHLFGLFINYLLINTLELINQFTFSSEALTMAFMLFSSTLLWNLIPILNSDGYKILLAFLSLDEYSRFKTNHWLVLTIQIIGIGLAVNSVVHWILYIVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	252 (208)
Sequences:	596 (502)
Seq/√Len:	34.8

BACSU - YYDH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
45_F	112_Y	9.093	1.00
39_D	115_K	4.239	1.00
53_S	113_S	4.205	1.00
109_G	161_I	3.870	1.00
156_L	208_I	3.763	1.00
41_Q	45_F	3.237	1.00
43_L	115_K	2.898	1.00
142_E	145_M	2.463	1.00
117_F	153_I	2.426	1.00
113_S	153_I	2.390	1.00
72_Y	170_E	2.327	0.99
105_L	161_I	2.264	0.99
148_R	214_S	2.248	0.99
108_L	124_V	2.207	0.99
114_L	119_K	2.204	0.99
108_L	112_Y	2.163	0.99
144_Y	211_A	2.132	0.99
153_I	160_F	2.123	0.99
172_I	176_T	2.109	0.99
64_T	164_L	2.102	0.99
48_Y	51_K	2.034	0.98
156_L	159_L	1.978	0.98
117_F	150_E	1.947	0.98
38_S	42_L	1.941	0.98
35_N	137_Y	1.914	0.98
162_N	202_N	1.894	0.97
57_F	61_L	1.856	0.97
41_Q	112_Y	1.823	0.97
32_N	128_L	1.733	0.96
119_K	142_E	1.725	0.96
143_T	154_V	1.719	0.95
162_N	207_K	1.661	0.94
199_P	205_G	1.659	0.94
42_L	111_I	1.658	0.94
152_I	212_F	1.649	0.94
42_L	124_V	1.616	0.94
134_P	205_G	1.608	0.93
72_Y	83_S	1.604	0.93
124_V	138_V	1.583	0.93
109_G	122_D	1.579	0.93
46_K	49_K	1.570	0.93
75_L	78_L	1.557	0.92
137_Y	205_G	1.547	0.92
119_K	146_L	1.529	0.92
92_W	96_V	1.524	0.91
42_L	121_F	1.523	0.91
49_K	112_Y	1.489	0.90
159_L	165_L	1.462	0.90
146_L	154_V	1.454	0.89
60_F	128_L	1.440	0.89
141_N	145_M	1.439	0.89
162_N	198_I	1.421	0.88
73_I	156_L	1.411	0.88
172_I	175_F	1.389	0.87
146_L	150_E	1.350	0.85
67_M	171_L	1.336	0.85
111_I	138_V	1.335	0.85
114_L	146_L	1.321	0.84
197_L	219_S	1.320	0.84
32_N	101_M	1.296	0.83
114_L	154_V	1.292	0.83
61_L	168_T	1.248	0.81
155_H	211_A	1.245	0.80
198_I	211_A	1.227	0.79
158_G	204_D	1.215	0.79
106_H	204_D	1.193	0.77
159_L	192_T	1.171	0.76
106_H	158_G	1.167	0.76
138_V	196_N	1.135	0.74
110_H	204_D	1.135	0.74
107_E	204_D	1.129	0.73
123_K	137_Y	1.124	0.73
129_N	134_P	1.124	0.73
110_H	158_G	1.108	0.72
107_E	158_G	1.103	0.72
103_I	166_I	1.101	0.72
207_K	211_A	1.099	0.71
66_L	94_I	1.093	0.71
60_F	168_T	1.091	0.71
106_H	110_H	1.087	0.71
37_L	80_N	1.070	0.69
188_L	193_L	1.069	0.69
150_E	153_I	1.062	0.69
58_Y	160_F	1.058	0.68
82_L	86_F	1.048	0.68
169_L	173_N	1.047	0.68
53_S	211_A	1.041	0.67
190_S	207_K	1.038	0.67
66_L	93_I	1.034	0.67
68_F	171_L	1.029	0.66
92_W	205_G	1.026	0.66
78_L	172_I	1.020	0.66
107_E	110_H	1.020	0.66
61_L	64_T	1.019	0.65
113_S	160_F	1.017	0.65
59_L	92_W	1.013	0.65
38_S	135_A	0.970	0.62
72_Y	79_Q	0.969	0.62
42_L	112_Y	0.963	0.61
213_L	216_D	0.956	0.60
39_D	43_L	0.954	0.60
103_I	162_N	0.953	0.60
68_F	174_Q	0.952	0.60
140_L	144_Y	0.944	0.59
60_F	63_F	0.942	0.59
49_K	53_S	0.939	0.59
144_Y	162_N	0.937	0.59
46_K	222_K	0.934	0.59
162_N	217_E	0.930	0.58
60_F	98_Y	0.908	0.56
68_F	167_N	0.905	0.56
56_F	59_L	0.904	0.56
137_Y	199_P	0.897	0.56
99_F	136_F	0.890	0.55
182_L	228_V	0.885	0.55
228_V	232_Q	0.885	0.55
58_Y	150_E	0.884	0.54
145_M	214_S	0.877	0.54
81_G	84_S	0.874	0.54
129_N	201_L	0.873	0.54
85_V	194_L	0.871	0.53
111_I	139_Q	0.871	0.53
61_L	164_L	0.870	0.53
94_I	180_E	0.866	0.53
219_S	223_T	0.863	0.53
165_L	169_L	0.855	0.52
129_N	135_A	0.852	0.52
123_K	139_Q	0.851	0.52
62_S	150_E	0.848	0.51
24_K	28_E	0.846	0.51
151_K	211_A	0.837	0.50
32_N	104_V	0.835	0.50
197_L	205_G	0.829	0.50
32_N	148_R	0.823	0.49
103_I	211_A	0.821	0.49
147_S	192_T	0.818	0.49
144_Y	213_L	0.816	0.49
127_K	135_A	0.815	0.49
154_V	196_N	0.814	0.48
103_I	173_N	0.809	0.48
86_F	200_I	0.807	0.48
172_I	181_A	0.803	0.48
157_F	161_I	0.802	0.47
68_F	139_Q	0.801	0.47
120_N	142_E	0.792	0.47
51_K	57_F	0.792	0.47
191_S	214_S	0.781	0.46
159_L	208_I	0.780	0.46
129_N	155_H	0.778	0.45
67_M	70_L	0.778	0.45
123_K	148_R	0.777	0.45
120_N	186_F	0.773	0.45
198_I	219_S	0.773	0.45
135_A	182_L	0.771	0.45
85_V	227_L	0.767	0.44
117_F	146_L	0.764	0.44
134_P	216_D	0.756	0.44
138_V	203_S	0.756	0.44
86_F	186_F	0.755	0.43
53_S	191_S	0.754	0.43
40_K	43_L	0.754	0.43
137_Y	203_S	0.753	0.43
60_F	93_I	0.750	0.43
157_F	222_K	0.747	0.43
141_N	198_I	0.744	0.43
100_I	132_V	0.743	0.42
141_N	219_S	0.741	0.42
44_R	112_Y	0.740	0.42
229_L	232_Q	0.737	0.42
119_K	154_V	0.736	0.42
228_V	231_I	0.728	0.41
60_F	65_A	0.725	0.41
60_F	64_T	0.723	0.41
122_D	228_V	0.723	0.41
138_V	200_I	0.722	0.41
131_Y	135_A	0.722	0.41
128_L	134_P	0.721	0.41
162_N	222_K	0.720	0.41
102_N	197_L	0.719	0.40
137_Y	196_N	0.714	0.40
202_N	207_K	0.711	0.40
91_M	138_V	0.710	0.40
39_D	52_V	0.706	0.39
196_N	203_S	0.706	0.39
58_Y	66_L	0.704	0.39
108_L	184_M	0.704	0.39
129_N	203_S	0.703	0.39
101_M	153_I	0.702	0.39
134_P	221_F	0.700	0.39
184_M	201_L	0.700	0.39
122_D	207_K	0.699	0.39
202_N	217_E	0.698	0.39
207_K	210_L	0.696	0.39
126_F	201_L	0.695	0.38
63_F	77_K	0.691	0.38
182_L	195_W	0.690	0.38
111_I	145_M	0.689	0.38
134_P	211_A	0.688	0.38
92_W	186_F	0.684	0.38
59_L	67_M	0.684	0.38
211_A	216_D	0.682	0.37
33_S	51_K	0.679	0.37
109_G	145_M	0.677	0.37
62_S	70_L	0.668	0.36
223_T	227_L	0.664	0.36
165_L	205_G	0.664	0.36
53_S	116_F	0.662	0.36
162_N	211_A	0.659	0.36
65_A	70_L	0.657	0.35
225_H	229_L	0.656	0.35
62_S	101_M	0.651	0.35
37_L	124_V	0.651	0.35
109_G	112_Y	0.651	0.35
55_K	73_I	0.649	0.35
162_N	192_T	0.648	0.35
69_I	73_I	0.647	0.35
114_L	135_A	0.646	0.35
45_F	55_K	0.644	0.34
79_Q	185_A	0.643	0.34
59_L	63_F	0.640	0.34
37_L	59_L	0.638	0.34
48_Y	112_Y	0.637	0.34
110_H	206_Y	0.637	0.34
132_V	182_L	0.637	0.34
76_I	80_N	0.632	0.34
63_F	147_S	0.627	0.33
196_N	205_G	0.626	0.33
39_D	119_K	0.625	0.33
139_Q	151_K	0.623	0.33
80_N	84_S	0.617	0.32
200_I	214_S	0.616	0.32
102_N	165_L	0.605	0.32
66_L	220_R	0.604	0.31
29_Y	202_N	0.603	0.31
77_K	170_E	0.603	0.31
137_Y	212_F	0.597	0.31
43_L	49_K	0.597	0.31
37_L	40_K	0.595	0.31
116_F	153_I	0.595	0.31
182_L	187_M	0.593	0.31
144_Y	219_S	0.593	0.31
144_Y	189_F	0.592	0.31
63_F	227_L	0.590	0.30
149_N	176_T	0.590	0.30
33_S	136_F	0.589	0.30
128_L	196_N	0.584	0.30
94_I	172_I	0.582	0.30
109_G	113_S	0.581	0.30
104_V	176_T	0.580	0.30
37_L	67_M	0.574	0.29
131_Y	211_A	0.573	0.29
24_K	29_Y	0.573	0.29
137_Y	173_N	0.572	0.29
60_F	174_Q	0.571	0.29
160_F	212_F	0.571	0.29
52_V	208_I	0.569	0.29
55_K	149_N	0.569	0.29
143_T	211_A	0.568	0.29
83_S	104_V	0.565	0.29
173_N	200_I	0.563	0.28
175_F	195_W	0.562	0.28
100_I	136_F	0.561	0.28
82_L	182_L	0.559	0.28
183_T	188_L	0.558	0.28
112_Y	222_K	0.557	0.28
94_I	229_L	0.557	0.28
113_S	154_V	0.556	0.28
60_F	96_V	0.556	0.28
62_S	187_M	0.556	0.28
52_V	69_I	0.553	0.28
100_I	141_N	0.552	0.28
162_N	201_L	0.552	0.28
89_W	104_V	0.550	0.28
162_N	189_F	0.550	0.28
62_S	66_L	0.549	0.28
60_F	194_L	0.548	0.27
109_G	185_A	0.548	0.27
192_T	196_N	0.546	0.27
60_F	66_L	0.545	0.27
192_T	202_N	0.544	0.27
63_F	174_Q	0.544	0.27
215_L	221_F	0.544	0.27
129_N	198_I	0.544	0.27
29_Y	128_L	0.540	0.27
57_F	141_N	0.539	0.27
195_W	198_I	0.538	0.27
209_L	213_L	0.537	0.27
192_T	195_W	0.536	0.27
210_L	217_E	0.534	0.27
46_K	105_L	0.534	0.27
190_S	194_L	0.531	0.26
39_D	122_D	0.531	0.26
93_I	172_I	0.530	0.26
49_K	160_F	0.529	0.26
105_L	113_S	0.526	0.26
123_K	225_H	0.525	0.26
51_K	55_K	0.524	0.26
155_H	214_S	0.524	0.26
152_I	155_H	0.522	0.26
203_S	211_A	0.519	0.26
138_V	221_F	0.518	0.25
52_V	56_F	0.518	0.25
76_I	108_L	0.517	0.25
39_D	44_R	0.515	0.25
108_L	210_L	0.514	0.25
128_L	213_L	0.513	0.25
50_E	116_F	0.512	0.25
30_Y	203_S	0.507	0.25
143_T	207_K	0.505	0.25
125_G	199_P	0.504	0.25
139_Q	222_K	0.504	0.25
51_K	93_I	0.500	0.24

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
3b4rA	2	0.75	99.7	0.721	Contact Map
2di4A	3	0.4722	10.2	0.959	Contact Map
3ilwA	2	0.2381	5.9	0.964	Contact Map
1vx7U	1	0.2302	3.7	0.967	Contact Map
3j39S	1	0.2341	3.6	0.967	Contact Map
4a18X	1	0.2381	3.2	0.968	Contact Map
2inrA	2	0.2421	2.7	0.969	Contact Map
3hsqA	3	0.2381	2.7	0.969	Contact Map
2xf7A	3	0.0913	2.7	0.969	Contact Map
3kvpA	3	0.119	2.4	0.97	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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