YDCG - BACSU - GREMLIN Contacts

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YDCG - UPF0310 protein YdcG

UniProt:	P96624	Sequences: MNTNYWIGVVSEQHVLKGAAGGFAQLCHGKKAPLAKMKEGDWLIYYSPRDAYPDGKLLRSFTAIGKVKSGNIYPYQMAPNFIPYRLDIDYYPCHKIGFYDIKSKLEFVQETKHLGFLFRRGHFEISKKDFLTIAQAMGVNISGMAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (135)
Sequences:	228 (164)
Seq/√Len:	14.1

BACSU - YDCG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_S	62_T	3.980	1.00
8_G	24_A	3.576	0.99
76_Q	79_P	3.573	0.99
8_G	26_L	3.113	0.98
10_V	43_L	2.934	0.97
127_K	131_L	2.818	0.96
31_K	35_A	2.588	0.94
24_A	45_Y	2.586	0.94
15_V	63_A	2.281	0.89
114_L	129_D	2.238	0.88
67_V	88_I	2.182	0.86
5_Y	130_F	2.158	0.86
115_G	129_D	2.139	0.85
108_V	113_H	2.122	0.85
7_I	123_F	2.098	0.84
69_S	87_D	2.076	0.83
75_Y	82_I	2.024	0.82
15_V	45_Y	2.020	0.81
37_M	122_H	1.963	0.79
50_D	55_G	1.942	0.79
4_N	124_E	1.902	0.77
55_G	58_L	1.758	0.71
107_F	118_F	1.748	0.71
84_Y	132_T	1.701	0.69
108_V	118_F	1.630	0.65
7_I	125_I	1.617	0.65
26_L	122_H	1.578	0.63
27_C	75_Y	1.558	0.62
37_M	130_F	1.489	0.58
49_R	55_G	1.399	0.53
12_E	113_H	1.354	0.51
73_Y	87_D	1.318	0.49
42_W	66_K	1.315	0.49
7_I	42_W	1.279	0.47
90_Y	108_V	1.247	0.45
27_C	33_P	1.246	0.45
14_H	28_H	1.239	0.44
12_E	58_L	1.237	0.44
90_Y	118_F	1.228	0.44
42_W	130_F	1.219	0.43
15_V	19_A	1.219	0.43
8_G	45_Y	1.218	0.43
21_G	43_L	1.218	0.43
107_F	125_I	1.194	0.42
7_I	118_F	1.186	0.42
98_F	133_I	1.184	0.41
8_G	122_H	1.154	0.40
25_Q	85_R	1.142	0.39
4_N	57_L	1.115	0.38
84_Y	99_Y	1.112	0.38
44_I	125_I	1.101	0.37
107_F	129_D	1.098	0.37
8_G	88_I	1.057	0.35
102_K	107_F	1.057	0.35
102_K	118_F	1.046	0.34
7_I	107_F	1.045	0.34
102_K	110_E	1.040	0.34
63_A	90_Y	1.028	0.34
32_A	67_V	1.009	0.33
47_S	61_F	1.004	0.32
72_I	124_E	1.000	0.32
96_I	100_D	0.998	0.32
62_T	125_I	0.996	0.32
54_D	57_L	0.991	0.32
74_P	82_I	0.987	0.32
5_Y	42_W	0.985	0.31
110_E	113_H	0.983	0.31
69_S	86_L	0.982	0.31
26_L	45_Y	0.980	0.31
43_L	107_F	0.980	0.31
5_Y	124_E	0.975	0.31
111_T	118_F	0.973	0.31
99_Y	102_K	0.969	0.31
50_D	58_L	0.966	0.31
15_V	90_Y	0.949	0.30
100_D	107_F	0.944	0.30
109_Q	127_K	0.943	0.30
105_L	129_D	0.936	0.29
65_G	97_G	0.928	0.29
12_E	95_K	0.911	0.28
107_F	123_F	0.909	0.28
106_E	126_S	0.899	0.28
19_A	90_Y	0.898	0.28
105_L	114_L	0.897	0.28
65_G	88_I	0.879	0.27
76_Q	80_N	0.878	0.27
101_I	133_I	0.871	0.26
23_F	36_K	0.870	0.26
5_Y	127_K	0.867	0.26
27_C	77_M	0.865	0.26
51_A	104_K	0.855	0.26
51_A	92_P	0.842	0.25
101_I	114_L	0.832	0.25
100_D	114_L	0.825	0.24
52_Y	123_F	0.822	0.24
108_V	111_T	0.820	0.24
62_T	86_L	0.801	0.24
26_L	32_A	0.798	0.23
8_G	43_L	0.797	0.23
35_A	92_P	0.795	0.23
109_Q	113_H	0.790	0.23
10_V	120_R	0.789	0.23
64_I	72_I	0.780	0.23
98_F	115_G	0.779	0.23
26_L	57_L	0.773	0.22
9_V	45_Y	0.772	0.22
30_K	40_G	0.753	0.22
63_A	118_F	0.745	0.21
68_K	87_D	0.744	0.21
37_M	49_R	0.742	0.21
86_L	121_G	0.740	0.21
10_V	49_R	0.736	0.21
116_F	120_R	0.735	0.21
106_E	128_K	0.734	0.21
63_A	130_F	0.730	0.21
12_E	16_L	0.730	0.21
25_Q	81_F	0.729	0.21
39_E	70_G	0.726	0.21
25_Q	28_H	0.724	0.21
15_V	24_A	0.720	0.21
7_I	31_K	0.717	0.20
15_V	62_T	0.716	0.20
24_A	37_M	0.714	0.20
14_H	25_Q	0.713	0.20
23_F	87_D	0.705	0.20
64_I	93_C	0.704	0.20
18_G	84_Y	0.694	0.20
27_C	85_R	0.692	0.20
94_H	97_G	0.692	0.20
13_Q	26_L	0.688	0.19
15_V	47_S	0.687	0.19
10_V	53_P	0.682	0.19
10_V	45_Y	0.681	0.19
27_C	81_F	0.680	0.19
98_F	114_L	0.674	0.19
98_F	102_K	0.670	0.19
23_F	78_A	0.668	0.19
80_N	120_R	0.667	0.19
10_V	17_K	0.663	0.19
10_V	51_A	0.662	0.19
59_R	120_R	0.650	0.18
51_A	112_K	0.649	0.18
58_L	138_G	0.642	0.18
47_S	64_I	0.639	0.18
124_E	127_K	0.637	0.18
101_I	129_D	0.634	0.18
52_Y	131_L	0.633	0.18
5_Y	89_D	0.629	0.17
59_R	123_F	0.625	0.17
62_T	124_E	0.619	0.17
20_A	51_A	0.618	0.17
101_I	115_G	0.614	0.17
47_S	86_L	0.607	0.17
4_N	72_I	0.607	0.17
70_G	106_E	0.600	0.17
74_P	84_Y	0.600	0.17
115_G	133_I	0.599	0.17
105_L	115_G	0.598	0.17
60_S	95_K	0.597	0.16
129_D	136_A	0.594	0.16
111_T	115_G	0.593	0.16
111_T	129_D	0.590	0.16
48_P	97_G	0.584	0.16
27_C	82_I	0.583	0.16
100_D	115_G	0.582	0.16
102_K	108_V	0.582	0.16
67_V	84_Y	0.581	0.16
131_L	138_G	0.575	0.16
95_K	111_T	0.573	0.16
82_I	109_Q	0.573	0.16
19_A	72_I	0.572	0.16
7_I	74_P	0.572	0.16
93_C	118_F	0.568	0.16
33_P	84_Y	0.565	0.16
15_V	44_I	0.562	0.15
51_A	54_D	0.560	0.15
26_L	87_D	0.553	0.15
83_P	137_M	0.552	0.15
47_S	63_A	0.551	0.15
66_K	135_Q	0.544	0.15
101_I	110_E	0.544	0.15
44_I	130_F	0.544	0.15
128_K	136_A	0.541	0.15
12_E	35_A	0.533	0.15
107_F	115_G	0.532	0.15
115_G	136_A	0.526	0.14
108_V	114_L	0.521	0.14
81_F	133_I	0.519	0.14
96_I	136_A	0.519	0.14
128_K	132_T	0.515	0.14
116_F	129_D	0.514	0.14
37_M	79_P	0.511	0.14
44_I	134_A	0.509	0.14
4_N	44_I	0.507	0.14
96_I	126_S	0.506	0.14
80_N	90_Y	0.506	0.14
19_A	56_K	0.505	0.14
66_K	91_Y	0.505	0.14
13_Q	132_T	0.503	0.14
78_A	87_D	0.501	0.14
60_S	86_L	0.500	0.14
50_D	99_Y	0.500	0.14

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
2hd9A	1	0.9315	100	0.572	Contact Map
2p5dA	1	0.911	100	0.597	Contact Map
1zceA	1	0.8699	96.4	0.903	Contact Map
2gbsA	1	0.863	95.4	0.911	Contact Map
2ar1A	1	0.863	95.3	0.911	Contact Map
2eveA	1	0.8219	94.3	0.916	Contact Map
4q4gX	1	0.589	45.3	0.949	Contact Map
3eopA	1	0.8425	21.5	0.957	Contact Map
3pbiA	1	0.5822	18.5	0.958	Contact Map
2wtpA	2	0.3493	15.1	0.96	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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