YUAD - BACSU - GREMLIN Contacts

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YUAD - Putative metal-sulfur cluster biosynthesis proteins YuaD

UniProt:	O32079	Sequences: MWKRMTAKAEGLYIADTKSFVTKQMDKLDFDYGGIPGDLHFGLTKKAGAREPMFSRGTEIFNRRQISIVSIEECNEIALKMGVPRILPEWLGANVAVSGMPDLTSLKEGSRIIFPSGAALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIVERPGAVYTGDEIEVHSYQRKVKRKAERV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (170)
Sequences:	146 (115)
Seq/√Len:	8.8

BACSU - YUAD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_M	179_H	5.302	1.00
104_T	125_E	3.943	0.98
30_F	66_I	3.564	0.96
104_T	184_K	3.277	0.93
70_S	73_E	2.992	0.90
127_D	182_Q	2.963	0.89
130_I	133_G	2.895	0.88
48_G	51_E	2.750	0.85
27_K	171_Y	2.366	0.75
137_Q	145_K	2.328	0.74
54_F	121_L	2.318	0.73
32_Y	167_P	2.168	0.68
91_L	132_P	2.061	0.64
29_D	169_A	1.977	0.61
71_I	98_S	1.945	0.59
35_I	94_N	1.893	0.57
109_G	124_G	1.891	0.57
104_T	157_I	1.834	0.55
97_V	155_L	1.828	0.54
33_G	43_L	1.824	0.54
114_F	118_A	1.805	0.53
47_A	123_E	1.777	0.52
120_L	164_V	1.718	0.50
49_A	56_R	1.635	0.46
75_N	79_L	1.622	0.46
69_V	93_A	1.599	0.45
39_L	135_V	1.584	0.44
54_F	116_S	1.551	0.43
103_L	106_L	1.543	0.42
170_V	176_I	1.530	0.42
54_F	115_P	1.514	0.41
16_D	39_L	1.502	0.40
95_V	106_L	1.494	0.40
119_A	163_I	1.490	0.40
106_L	170_V	1.487	0.40
77_I	81_M	1.478	0.39
90_W	135_V	1.469	0.39
67_S	133_G	1.460	0.39
52_P	179_H	1.434	0.38
61_F	163_I	1.429	0.38
86_I	93_A	1.388	0.36
81_M	104_T	1.379	0.36
39_L	167_P	1.377	0.35
133_G	167_P	1.372	0.35
113_I	163_I	1.372	0.35
31_D	167_P	1.355	0.35
38_D	114_F	1.354	0.35
69_V	100_M	1.339	0.34
111_R	166_R	1.331	0.34
28_L	81_M	1.328	0.34
20_F	38_D	1.305	0.33
45_K	181_Y	1.305	0.33
109_G	178_V	1.270	0.31
41_F	59_E	1.253	0.31
136_I	144_P	1.236	0.30
45_K	107_K	1.215	0.29
71_I	180_S	1.209	0.29
30_F	167_P	1.202	0.29
31_D	47_A	1.187	0.28
66_I	84_P	1.172	0.28
66_I	134_E	1.163	0.28
33_G	167_P	1.149	0.27
86_I	90_W	1.149	0.27
72_E	111_R	1.140	0.27
127_D	132_P	1.111	0.26
66_I	162_C	1.108	0.26
67_S	74_C	1.104	0.26
151_V	157_I	1.098	0.25
27_K	169_A	1.091	0.25
15_A	94_N	1.076	0.25
113_I	119_A	1.073	0.25
27_K	101_P	1.073	0.25
15_A	18_K	1.072	0.25
15_A	39_L	1.067	0.24
28_L	35_I	1.054	0.24
32_Y	36_P	1.046	0.24
80_K	138_S	1.043	0.24
114_F	170_V	1.042	0.24
134_E	137_Q	1.037	0.23
71_I	85_R	1.023	0.23
90_W	165_E	1.020	0.23
106_L	133_G	1.006	0.22
97_V	101_P	1.005	0.22
47_A	58_T	1.004	0.22
66_I	132_P	1.002	0.22
16_D	167_P	0.998	0.22
76_E	157_I	0.997	0.22
19_S	138_S	0.996	0.22
71_I	76_E	0.994	0.22
83_V	155_L	0.993	0.22
136_I	165_E	0.981	0.22
79_L	106_L	0.975	0.22
124_G	184_K	0.969	0.21
82_G	105_S	0.963	0.21
22_T	81_M	0.963	0.21
24_Q	97_V	0.951	0.21
47_A	174_D	0.951	0.21
123_E	131_Q	0.948	0.21
107_K	181_Y	0.946	0.21
54_F	97_V	0.945	0.21
157_I	177_E	0.922	0.20
38_D	46_K	0.914	0.20
33_G	94_N	0.914	0.20
22_T	97_V	0.912	0.20
37_G	80_K	0.910	0.20
77_I	150_F	0.903	0.20
45_K	61_F	0.903	0.20
53_M	121_L	0.903	0.20
67_S	95_V	0.888	0.19
59_E	167_P	0.880	0.19
114_F	176_I	0.873	0.19
116_S	146_L	0.866	0.19
67_S	130_I	0.863	0.18
87_L	101_P	0.858	0.18
72_E	177_E	0.855	0.18
51_E	186_K	0.854	0.18
86_I	91_L	0.847	0.18
59_E	156_G	0.844	0.18
25_M	28_L	0.833	0.18
32_Y	182_Q	0.831	0.18
114_F	146_L	0.830	0.18
167_P	172_T	0.829	0.18
55_S	82_G	0.829	0.18
121_L	177_E	0.825	0.18
101_P	164_V	0.820	0.17
113_I	179_H	0.817	0.17
19_S	77_I	0.815	0.17
122_C	160_I	0.814	0.17
69_V	86_I	0.812	0.17
98_S	175_E	0.811	0.17
53_M	160_I	0.811	0.17
88_P	131_Q	0.810	0.17
87_L	149_A	0.808	0.17
30_F	95_V	0.800	0.17
72_E	166_R	0.793	0.17
21_V	139_Y	0.788	0.17
17_T	122_C	0.781	0.16
25_M	185_V	0.781	0.16
49_A	80_K	0.775	0.16
126_N	158_R	0.774	0.16
129_C	158_R	0.774	0.16
126_N	129_C	0.774	0.16
21_V	135_V	0.767	0.16
45_K	108_E	0.751	0.16
119_A	134_E	0.751	0.16
35_I	81_M	0.750	0.16
54_F	100_M	0.745	0.16
46_K	80_K	0.744	0.16
124_G	161_V	0.742	0.16
38_D	161_V	0.735	0.15
61_F	142_D	0.728	0.15
63_R	118_A	0.725	0.15
56_R	90_W	0.717	0.15
123_E	163_I	0.716	0.15
44_T	152_R	0.714	0.15
41_F	53_M	0.710	0.15
74_C	77_I	0.708	0.15
22_T	160_I	0.704	0.15
113_I	178_V	0.702	0.15
162_C	181_Y	0.702	0.15
138_S	171_Y	0.701	0.15
41_F	155_L	0.695	0.15
38_D	109_G	0.692	0.14
28_L	32_Y	0.691	0.14
40_H	129_C	0.690	0.14
40_H	158_R	0.690	0.14
40_H	126_N	0.690	0.14
22_T	135_V	0.689	0.14
128_P	158_R	0.688	0.14
63_R	124_G	0.686	0.14
151_V	170_V	0.679	0.14
51_E	113_I	0.676	0.14
58_T	157_I	0.675	0.14
33_G	120_L	0.674	0.14
51_E	178_V	0.668	0.14
25_M	76_E	0.666	0.14
103_L	152_R	0.662	0.14
22_T	106_L	0.662	0.14
48_G	182_Q	0.657	0.14
31_D	115_P	0.657	0.14
45_K	112_I	0.651	0.14
70_S	176_I	0.648	0.14
30_F	175_E	0.648	0.14
37_G	122_C	0.645	0.13
28_L	94_N	0.644	0.13
26_D	97_V	0.640	0.13
22_T	35_I	0.635	0.13
63_R	109_G	0.634	0.13
97_V	143_Q	0.628	0.13
66_I	69_V	0.626	0.13
121_L	179_H	0.620	0.13
28_L	33_G	0.617	0.13
97_V	103_L	0.614	0.13
54_F	94_N	0.614	0.13
69_V	155_L	0.610	0.13
25_M	83_V	0.609	0.13
91_L	134_E	0.603	0.13
40_H	128_P	0.602	0.13
91_L	137_Q	0.599	0.13
21_V	124_G	0.597	0.13
32_Y	174_D	0.596	0.13
59_E	101_P	0.596	0.13
18_K	131_Q	0.594	0.12
21_V	106_L	0.593	0.12
51_E	121_L	0.588	0.12
143_Q	185_V	0.588	0.12
67_S	114_F	0.587	0.12
31_D	120_L	0.586	0.12
112_I	153_H	0.586	0.12
125_E	184_K	0.583	0.12
77_I	85_R	0.577	0.12
44_T	179_H	0.572	0.12
132_P	136_I	0.571	0.12
89_E	101_P	0.568	0.12
147_A	178_V	0.568	0.12
77_I	131_Q	0.567	0.12
24_Q	79_L	0.563	0.12
19_S	170_V	0.560	0.12
109_G	123_E	0.559	0.12
44_T	53_M	0.557	0.12
90_W	143_Q	0.556	0.12
71_I	96_A	0.554	0.12
20_F	48_G	0.552	0.12
20_F	124_G	0.552	0.12
35_I	41_F	0.552	0.12
163_I	178_V	0.548	0.12
21_V	94_N	0.542	0.12
68_I	81_M	0.541	0.12
77_I	91_L	0.540	0.12
104_T	169_A	0.540	0.12
27_K	122_C	0.538	0.11
116_S	138_S	0.536	0.11
58_T	62_N	0.535	0.11
47_A	81_M	0.534	0.11
108_E	123_E	0.534	0.11
43_L	52_P	0.534	0.11
41_F	55_S	0.534	0.11
28_L	135_V	0.531	0.11
59_E	84_P	0.527	0.11
156_G	184_K	0.526	0.11
44_T	59_E	0.525	0.11
19_S	39_L	0.522	0.11
103_L	172_T	0.522	0.11
41_F	122_C	0.521	0.11
113_I	186_K	0.518	0.11
99_G	173_G	0.515	0.11
133_G	152_R	0.515	0.11
121_L	135_V	0.515	0.11
144_P	167_P	0.512	0.11
84_P	185_V	0.509	0.11
66_I	83_V	0.508	0.11
28_L	174_D	0.507	0.11
52_P	133_G	0.501	0.11
79_L	84_P	0.500	0.11
68_I	176_I	0.500	0.11

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
1oruA	2	0.9479	100	0.615	Contact Map
1o65A	1	0.8438	99.8	0.77	Contact Map
1l8nA	2	0.8854	43.2	0.961	Contact Map
3b02A	2	0.4323	20.5	0.967	Contact Map
3tg2A	2	0.5052	19.1	0.967	Contact Map
4ev0A	2	0.401	16	0.969	Contact Map
4h17A	2	0.4635	15.9	0.969	Contact Map
4cydA	2	0.401	15.2	0.969	Contact Map
3mcwA	2	0.4219	15.2	0.969	Contact Map
3dkwA	2	0.3958	14.9	0.969	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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