GERD - BACSU - GREMLIN Contacts

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GERD - Spore germination protein GerD

UniProt:	P16450	Sequences: MSKAKTLLMSCFLLLSVTACAPKDQAADMDYDQTKKMVVDILKTDDGKKAIKELLNDDAMNEALVIDQDAIKGTIEKTLTSKKGEEFWKNIFEDTDFAEGFAKTLQTEHEKVIKKLMKDPDYQKMLMSVMQDPGMDKKYSQLAKSQEFRSYLEEVINETLSSPLYKKQFEDELKKAAKDTAKESE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (175)
Sequences:	185 (149)
Seq/√Len:	11.3

BACSU - GERD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_L	129_V	5.123	1.00
90_N	93_E	3.743	0.99
124_K	146_Q	3.311	0.97
86_E	89_K	2.662	0.90
19_A	127_M	2.527	0.88
141_Q	145_S	2.431	0.86
130_M	158_E	2.392	0.85
99_E	103_K	2.360	0.84
38_V	41_I	2.358	0.84
91_I	143_A	2.267	0.81
36_K	88_W	2.255	0.81
137_K	155_V	2.233	0.80
128_S	131_Q	2.200	0.79
46_D	93_E	2.172	0.78
126_L	165_Y	2.064	0.74
153_E	159_T	2.051	0.74
13_L	107_T	2.015	0.73
148_F	156_I	1.998	0.72
135_M	139_Y	1.957	0.70
148_F	151_Y	1.951	0.70
17_V	158_E	1.923	0.69
56_N	161_S	1.907	0.68
152_L	156_I	1.883	0.67
39_V	147_E	1.867	0.67
169_F	173_L	1.850	0.66
126_L	135_M	1.829	0.65
123_Q	146_Q	1.825	0.65
120_P	153_E	1.731	0.60
112_V	126_L	1.707	0.59
128_S	144_K	1.704	0.59
109_H	113_I	1.698	0.59
61_N	64_L	1.674	0.58
19_A	25_Q	1.672	0.58
55_L	85_E	1.671	0.58
22_P	148_F	1.604	0.54
117_M	126_L	1.586	0.54
98_A	120_P	1.580	0.53
145_S	151_Y	1.566	0.53
123_Q	132_D	1.562	0.52
26_A	52_K	1.554	0.52
49_K	143_A	1.519	0.50
98_A	148_F	1.519	0.50
142_L	145_S	1.471	0.48
46_D	143_A	1.462	0.48
19_A	46_D	1.449	0.47
19_A	110_E	1.428	0.46
39_V	173_L	1.396	0.44
77_K	91_I	1.383	0.44
137_K	172_E	1.371	0.43
24_D	74_T	1.358	0.42
161_S	168_Q	1.350	0.42
114_K	122_Y	1.322	0.41
63_A	179_D	1.274	0.39
123_Q	128_S	1.262	0.38
39_V	50_A	1.260	0.38
96_D	103_K	1.254	0.38
48_K	55_L	1.248	0.37
88_W	104_T	1.239	0.37
85_E	107_T	1.234	0.37
46_D	49_K	1.232	0.37
132_D	145_S	1.224	0.36
111_K	126_L	1.219	0.36
123_Q	138_K	1.211	0.36
57_D	71_I	1.207	0.36
90_N	164_L	1.203	0.35
98_A	118_K	1.197	0.35
115_K	142_L	1.184	0.35
10_S	19_A	1.181	0.34
14_L	51_I	1.169	0.34
94_D	97_F	1.159	0.33
39_V	81_S	1.142	0.33
53_E	126_L	1.133	0.32
72_K	123_Q	1.107	0.31
43_K	171_D	1.096	0.31
89_K	93_E	1.094	0.31
132_D	136_D	1.072	0.30
76_E	83_K	1.067	0.30
96_D	99_E	1.054	0.29
175_K	178_K	1.053	0.29
29_M	165_Y	1.039	0.28
67_D	102_A	1.033	0.28
46_D	141_Q	1.030	0.28
46_D	92_F	1.026	0.28
129_V	136_D	1.023	0.28
111_K	115_K	1.013	0.27
136_D	158_E	1.008	0.27
25_Q	53_E	1.005	0.27
28_D	162_S	0.984	0.26
137_K	164_L	0.974	0.26
113_I	125_M	0.962	0.25
141_Q	153_E	0.937	0.25
92_F	109_H	0.936	0.25
123_Q	129_V	0.936	0.25
48_K	88_W	0.916	0.24
82_K	131_Q	0.916	0.24
21_A	74_T	0.914	0.24
68_Q	74_T	0.914	0.24
58_D	71_I	0.914	0.24
84_G	88_W	0.912	0.24
121_D	160_L	0.905	0.23
105_L	112_V	0.902	0.23
8_L	13_L	0.901	0.23
73_G	77_K	0.897	0.23
67_D	127_M	0.893	0.23
47_G	159_T	0.888	0.23
173_L	177_A	0.888	0.23
72_K	168_Q	0.885	0.23
9_M	16_S	0.877	0.22
34_T	87_F	0.876	0.22
18_T	82_K	0.872	0.22
127_M	134_G	0.868	0.22
130_M	142_L	0.866	0.22
59_A	171_D	0.865	0.22
67_D	158_E	0.858	0.22
49_K	90_N	0.854	0.22
61_N	164_L	0.840	0.21
51_I	145_S	0.837	0.21
147_E	173_L	0.837	0.21
36_K	48_K	0.836	0.21
82_K	85_E	0.833	0.21
12_F	77_K	0.831	0.21
139_Y	166_K	0.830	0.21
8_L	93_E	0.825	0.21
11_C	158_E	0.814	0.20
30_D	121_D	0.807	0.20
9_M	56_N	0.805	0.20
73_G	129_V	0.802	0.20
90_N	159_T	0.799	0.20
31_Y	35_K	0.790	0.20
120_P	149_R	0.786	0.20
128_S	146_Q	0.779	0.19
12_F	16_S	0.777	0.19
98_A	146_Q	0.776	0.19
88_W	167_K	0.776	0.19
101_F	123_Q	0.775	0.19
32_D	36_K	0.771	0.19
169_F	172_E	0.769	0.19
78_T	147_E	0.766	0.19
87_F	91_I	0.766	0.19
14_L	127_M	0.764	0.19
156_I	160_L	0.762	0.19
132_D	146_Q	0.761	0.19
37_M	41_I	0.760	0.19
39_V	121_D	0.754	0.19
45_D	48_K	0.751	0.18
144_K	147_E	0.751	0.18
32_D	88_W	0.747	0.18
34_T	37_M	0.746	0.18
24_D	44_T	0.739	0.18
141_Q	154_E	0.732	0.18
148_F	161_S	0.728	0.18
155_V	160_L	0.725	0.18
29_M	150_S	0.721	0.18
21_A	79_L	0.721	0.18
120_P	131_Q	0.721	0.18
96_D	164_L	0.713	0.17
148_F	153_E	0.710	0.17
48_K	87_F	0.707	0.17
127_M	135_M	0.704	0.17
49_K	133_P	0.700	0.17
18_T	58_D	0.700	0.17
46_D	50_A	0.699	0.17
25_Q	63_A	0.698	0.17
51_I	91_I	0.695	0.17
77_K	154_E	0.692	0.17
37_M	97_F	0.688	0.17
74_T	146_Q	0.687	0.17
86_E	93_E	0.686	0.17
39_V	59_A	0.685	0.17
105_L	113_I	0.683	0.17
89_K	92_F	0.678	0.16
53_E	134_G	0.674	0.16
25_Q	134_G	0.674	0.16
126_L	171_D	0.674	0.16
19_A	173_L	0.666	0.16
92_F	176_A	0.665	0.16
78_T	125_M	0.660	0.16
145_S	176_A	0.659	0.16
27_A	148_F	0.658	0.16
91_I	171_D	0.658	0.16
148_F	179_D	0.654	0.16
108_E	111_K	0.652	0.16
19_A	78_T	0.650	0.16
21_A	101_F	0.647	0.16
106_Q	110_E	0.647	0.16
47_G	54_L	0.643	0.16
9_M	72_K	0.641	0.15
127_M	139_Y	0.640	0.15
108_E	131_Q	0.635	0.15
30_D	58_D	0.633	0.15
79_L	130_M	0.632	0.15
125_M	146_Q	0.629	0.15
75_I	179_D	0.628	0.15
34_T	47_G	0.626	0.15
89_K	117_M	0.625	0.15
15_L	160_L	0.619	0.15
53_E	85_E	0.613	0.15
76_E	154_E	0.613	0.15
125_M	132_D	0.612	0.15
151_Y	159_T	0.611	0.15
46_D	61_N	0.610	0.15
72_K	77_K	0.607	0.15
112_V	175_K	0.607	0.15
41_I	103_K	0.607	0.15
51_I	81_S	0.603	0.15
71_I	127_M	0.598	0.14
68_Q	96_D	0.597	0.14
15_L	148_F	0.597	0.14
49_K	176_A	0.593	0.14
21_A	135_M	0.591	0.14
9_M	12_F	0.590	0.14
109_H	129_V	0.589	0.14
95_T	102_A	0.588	0.14
57_D	92_F	0.585	0.14
11_C	14_L	0.583	0.14
74_T	110_E	0.580	0.14
68_Q	166_K	0.578	0.14
54_L	70_A	0.577	0.14
7_L	71_I	0.576	0.14
103_K	164_L	0.573	0.14
69_D	143_A	0.572	0.14
78_T	110_E	0.567	0.14
109_H	146_Q	0.567	0.14
123_Q	135_M	0.566	0.14
118_K	125_M	0.564	0.14
47_G	128_S	0.562	0.14
80_T	164_L	0.560	0.14
18_T	170_E	0.557	0.13
160_L	178_K	0.557	0.13
52_K	90_N	0.555	0.13
169_F	174_K	0.555	0.13
106_Q	154_E	0.555	0.13
43_K	160_L	0.554	0.13
137_K	162_S	0.552	0.13
44_T	51_I	0.550	0.13
69_D	100_G	0.549	0.13
23_K	77_K	0.546	0.13
118_K	128_S	0.545	0.13
63_A	143_A	0.544	0.13
108_E	157_N	0.544	0.13
16_S	22_P	0.539	0.13
124_K	127_M	0.539	0.13
41_I	175_K	0.535	0.13
82_K	86_E	0.535	0.13
19_A	22_P	0.534	0.13
148_F	152_L	0.529	0.13
153_E	157_N	0.527	0.13
90_N	175_K	0.526	0.13
142_L	167_K	0.526	0.13
123_Q	160_L	0.519	0.13
14_L	28_D	0.519	0.13
30_D	108_E	0.517	0.13
96_D	170_E	0.516	0.13
60_M	178_K	0.515	0.13
149_R	155_V	0.511	0.12
166_K	174_K	0.511	0.12
46_D	95_T	0.510	0.12
129_V	181_A	0.506	0.12
105_L	135_M	0.503	0.12
66_I	125_M	0.503	0.12
33_Q	65_V	0.502	0.12
33_Q	164_L	0.500	0.12

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
4o8wA	3	0.6541	100	0.459	Contact Map
2llwA	1	0.3838	92.2	0.925	Contact Map
2lnmA	1	0.3351	88.8	0.93	Contact Map
2llvA	1	0.3784	87.5	0.932	Contact Map
4r2fA	1	0.5243	34.2	0.954	Contact Map
4mfiA	1	0.7892	27.7	0.956	Contact Map
4kysA	1	0.4108	25.9	0.957	Contact Map
3zbiC	1	0.1459	25.8	0.957	Contact Map
3ombA	1	0.7676	21.1	0.959	Contact Map
2bptA	1	0.6054	21	0.959	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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