YRDA - BACSU - GREMLIN Contacts

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YRDA - Uncharacterized protein YrdA

UniProt:	O07079	Sequences: MFQTLDHFLKSWEFEADATQKLLNSLTDESLKQEITSQNWTLGRIAWHTVAAIGIITSNTDLTFQAPAEDYPVPTSAQFIADSYHQASNAFVQALKTQWTDHTLQERINFIGQQMPNGSLLMFLIQHQNHHRGQMTVLMRQAGLTVPGIYGPAKEEWAKFGLEAPKM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	167 (143)
Sequences:	617 (519)
Seq/√Len:	43.4

BACSU - YRDA YJOA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
103_T	106_E	3.875	1.00
78_Q	82_D	3.564	1.00
107_R	114_Q	3.345	1.00
109_N	114_Q	2.833	1.00
76_S	79_F	2.552	1.00
24_N	85_H	2.511	1.00
82_D	86_Q	2.505	1.00
13_E	92_V	2.439	1.00
100_T	103_T	2.295	1.00
89_N	93_Q	2.291	1.00
20_Q	24_N	2.221	1.00
11_S	122_M	2.179	1.00
133_G	136_T	2.161	1.00
81_A	85_H	2.094	0.99
19_T	132_R	2.077	0.99
24_N	81_A	1.995	0.99
34_E	41_T	1.962	0.99
48_H	127_H	1.803	0.98
28_D	78_Q	1.763	0.98
15_E	126_Q	1.735	0.98
116_P	119_S	1.718	0.98
92_V	96_K	1.698	0.97
79_F	82_D	1.694	0.97
31_L	80_I	1.663	0.97
86_Q	90_A	1.655	0.97
20_Q	85_H	1.646	0.97
9_L	96_K	1.622	0.97
7_H	118_G	1.590	0.96
50_V	53_I	1.486	0.95
37_S	143_G	1.474	0.94
26_L	77_A	1.459	0.94
127_H	133_G	1.459	0.94
110_F	120_L	1.438	0.93
33_Q	141_Q	1.418	0.93
107_R	116_P	1.408	0.93
33_Q	142_A	1.403	0.93
56_I	60_T	1.375	0.92
31_L	46_A	1.372	0.92
35_I	138_L	1.348	0.91
57_T	60_T	1.345	0.91
9_L	92_V	1.315	0.90
31_L	43_G	1.314	0.90
34_E	37_S	1.308	0.90
46_A	135_M	1.276	0.89
115_M	120_L	1.244	0.87
36_T	39_N	1.240	0.87
23_L	50_V	1.207	0.86
132_R	139_M	1.203	0.85
41_T	44_R	1.182	0.84
8_F	121_L	1.180	0.84
88_S	128_Q	1.164	0.83
28_D	77_A	1.155	0.83
21_K	24_N	1.151	0.83
6_D	10_K	1.137	0.82
18_A	149_I	1.136	0.82
107_R	110_F	1.130	0.82
27_T	147_P	1.115	0.81
23_L	46_A	1.096	0.80
23_L	31_L	1.085	0.79
22_L	133_G	1.084	0.79
130_H	134_Q	1.076	0.78
34_E	84_Y	1.069	0.78
16_A	128_Q	1.055	0.77
115_M	119_S	1.039	0.76
20_Q	81_A	1.039	0.76
49_T	135_M	1.036	0.76
136_T	149_I	1.034	0.75
13_E	96_K	1.031	0.75
42_L	77_A	1.026	0.75
16_A	88_S	1.023	0.75
55_I	111_I	0.997	0.73
10_K	119_S	0.994	0.72
42_L	45_I	0.971	0.71
26_L	31_L	0.968	0.70
31_L	77_A	0.968	0.70
45_I	79_F	0.968	0.70
69_E	79_F	0.967	0.70
9_L	93_Q	0.953	0.69
35_I	135_M	0.947	0.69
50_V	87_A	0.937	0.68
23_L	84_Y	0.937	0.68
127_H	136_T	0.936	0.68
45_I	134_Q	0.936	0.68
30_S	142_A	0.927	0.67
56_I	123_F	0.924	0.67
84_Y	128_Q	0.920	0.67
40_W	123_F	0.914	0.66
83_S	86_Q	0.894	0.64
15_E	18_A	0.892	0.64
101_D	118_G	0.890	0.64
27_T	77_A	0.890	0.64
96_K	129_N	0.889	0.64
74_P	79_F	0.882	0.63
138_L	142_A	0.881	0.63
26_L	139_M	0.878	0.63
6_D	25_S	0.876	0.63
93_Q	98_Q	0.873	0.62
19_T	36_T	0.861	0.61
78_Q	102_H	0.847	0.60
27_T	30_S	0.845	0.60
25_S	146_V	0.838	0.59
34_E	141_Q	0.832	0.59
138_L	141_Q	0.831	0.59
26_L	42_L	0.831	0.59
42_L	135_M	0.825	0.58
77_A	81_A	0.818	0.57
42_L	146_V	0.815	0.57
93_Q	96_K	0.808	0.56
11_S	126_Q	0.804	0.56
17_D	109_N	0.801	0.56
113_Q	122_M	0.797	0.55
146_V	149_I	0.793	0.55
15_E	88_S	0.792	0.55
51_A	69_E	0.791	0.55
126_Q	129_N	0.785	0.54
47_W	80_I	0.783	0.54
88_S	125_I	0.780	0.54
12_W	39_N	0.774	0.53
22_L	146_V	0.771	0.53
73_V	121_L	0.769	0.53
10_K	17_D	0.766	0.52
76_S	107_R	0.761	0.52
55_I	113_Q	0.760	0.52
60_T	110_F	0.759	0.52
70_D	102_H	0.756	0.51
94_A	98_Q	0.751	0.51
37_S	107_R	0.746	0.51
41_T	48_H	0.745	0.50
34_E	138_L	0.742	0.50
15_E	132_R	0.740	0.50
22_L	149_I	0.740	0.50
79_F	83_S	0.733	0.49
15_E	128_Q	0.731	0.49
27_T	81_A	0.721	0.48
82_D	100_T	0.701	0.46
39_N	126_Q	0.697	0.46
52_A	113_Q	0.697	0.46
62_L	101_D	0.693	0.45
108_I	117_N	0.691	0.45
52_A	55_I	0.690	0.45
23_L	26_L	0.688	0.45
127_H	149_I	0.679	0.44
32_K	93_Q	0.677	0.44
55_I	59_N	0.672	0.44
39_N	135_M	0.668	0.43
7_H	137_V	0.666	0.43
33_Q	138_L	0.661	0.42
26_L	127_H	0.660	0.42
137_V	141_Q	0.658	0.42
54_G	94_A	0.655	0.42
9_L	89_N	0.652	0.42
120_L	124_L	0.645	0.41
51_A	55_I	0.643	0.41
22_L	143_G	0.636	0.40
41_T	78_Q	0.633	0.40
48_H	52_A	0.629	0.40
19_T	139_M	0.628	0.39
73_V	76_S	0.627	0.39
108_I	116_P	0.627	0.39
61_D	100_T	0.626	0.39
6_D	83_S	0.625	0.39
99_W	139_M	0.615	0.38
22_L	60_T	0.608	0.38
43_G	133_G	0.607	0.38
28_D	31_L	0.603	0.37
12_W	128_Q	0.601	0.37
108_I	120_L	0.601	0.37
25_S	147_P	0.600	0.37
31_L	74_P	0.597	0.37
81_A	102_H	0.596	0.37
72_P	90_A	0.593	0.36
11_S	119_S	0.590	0.36
64_F	91_F	0.587	0.36
46_A	80_I	0.583	0.35
41_T	58_S	0.582	0.35
39_N	146_V	0.581	0.35
19_T	23_L	0.581	0.35
36_T	141_Q	0.578	0.35
75_T	82_D	0.573	0.35
40_W	44_R	0.572	0.34
58_S	144_L	0.569	0.34
24_N	77_A	0.568	0.34
45_I	140_R	0.566	0.34
109_N	121_L	0.565	0.34
75_T	86_Q	0.565	0.34
135_M	147_P	0.564	0.34
83_S	87_A	0.561	0.34
25_S	143_G	0.560	0.33
18_A	88_S	0.560	0.33
120_L	123_F	0.558	0.33
78_Q	89_N	0.551	0.33
104_L	136_T	0.550	0.33
6_D	93_Q	0.549	0.32
63_T	105_Q	0.546	0.32
35_I	38_Q	0.544	0.32
76_S	118_G	0.544	0.32
49_T	68_A	0.543	0.32
145_T	148_G	0.537	0.31
63_T	108_I	0.536	0.31
56_I	115_M	0.530	0.31
106_E	144_L	0.530	0.31
47_W	73_V	0.525	0.31
52_A	111_I	0.524	0.30
35_I	45_I	0.524	0.30
61_D	64_F	0.520	0.30
41_T	72_P	0.517	0.30
30_S	33_Q	0.516	0.30
6_D	96_K	0.513	0.30
56_I	124_L	0.507	0.29
6_D	57_T	0.506	0.29
36_T	139_M	0.503	0.29
18_A	146_V	0.503	0.29
49_T	109_N	0.501	0.29
21_K	64_F	0.500	0.29

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
3di5A	1	0.8982	100	0.451	Contact Map
2p1aA	2	0.8563	99.9	0.566	Contact Map
3dkaA	2	0.8802	99.9	0.595	Contact Map
2f22A	2	0.8563	99.9	0.599	Contact Map
2hkvA	2	0.8802	99.9	0.608	Contact Map
3gorA	2	0.9042	99.9	0.61	Contact Map
2qnlA	2	0.8263	99.8	0.63	Contact Map
2qe9A	2	0.9521	99.8	0.637	Contact Map
2ou6A	2	0.8383	99.8	0.647	Contact Map
3cexA	2	0.8563	99.8	0.661	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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