YYAB - BACSU - GREMLIN Contacts

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YYAB - Uncharacterized protein YyaB

UniProt:	P37523	Sequences: MVYQTKRDVPVTLMIVFLILLIQADAIVPFVLGNMRVSGWIIFILLTLLNGLIIWSFIDLKYVLKEHHLIIKAGLIKHQIPYENIDKVVQKKKLWSGFRLIGSRHAITIYYQGGWGHAVISPQKSEEFIHKLKEKNSNIIIFTKSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	146 (131)
Sequences:	276 (239)
Seq/√Len:	20.9

BACSU - YYAB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_N	139_I	4.229	1.00
55_W	75_L	4.070	1.00
105_H	125_S	3.492	1.00
60_L	102_G	3.384	1.00
82_Y	136_N	3.038	0.99
2_V	61_K	2.961	0.99
80_I	111_Y	2.874	0.99
64_L	82_Y	2.795	0.99
124_K	127_E	2.706	0.99
5_T	121_S	2.617	0.98
3_Y	131_K	2.395	0.97
82_Y	135_K	2.317	0.96
131_K	134_E	2.127	0.94
97_G	106_A	2.093	0.93
60_L	73_A	2.022	0.92
106_A	119_V	1.860	0.88
55_W	59_D	1.843	0.88
108_T	117_H	1.840	0.88
89_V	108_T	1.822	0.87
91_K	119_V	1.711	0.84
101_I	106_A	1.644	0.81
103_S	106_A	1.637	0.81
20_L	109_I	1.630	0.81
62_Y	122_P	1.617	0.80
88_V	132_L	1.577	0.78
90_Q	125_S	1.555	0.77
5_T	60_L	1.550	0.77
71_I	108_T	1.515	0.75
10_P	103_S	1.363	0.67
112_Q	116_G	1.358	0.67
95_W	119_V	1.336	0.66
2_V	63_V	1.266	0.61
82_Y	139_I	1.262	0.61
87_K	132_L	1.244	0.60
68_H	86_D	1.234	0.59
71_I	120_I	1.222	0.59
6_K	105_H	1.221	0.59
5_T	62_Y	1.189	0.56
68_H	79_Q	1.176	0.56
91_K	108_T	1.174	0.55
51_G	55_W	1.166	0.55
60_L	107_I	1.165	0.55
88_V	107_I	1.155	0.54
16_V	57_F	1.138	0.53
18_L	52_L	1.120	0.52
96_S	119_V	1.117	0.52
87_K	93_K	1.111	0.51
91_K	96_S	1.097	0.50
96_S	106_A	1.072	0.49
6_K	103_S	1.072	0.49
91_K	103_S	1.054	0.48
71_I	106_A	1.041	0.47
87_K	110_Y	1.023	0.46
97_G	119_V	1.022	0.45
53_I	84_N	1.015	0.45
103_S	125_S	1.014	0.45
95_W	103_S	1.009	0.45
57_F	102_G	1.002	0.44
15_I	53_I	0.993	0.44
14_M	18_L	0.993	0.44
82_Y	100_L	0.975	0.42
42_I	129_I	0.970	0.42
78_H	106_A	0.956	0.41
7_R	16_V	0.954	0.41
94_L	97_G	0.951	0.41
88_V	116_G	0.947	0.41
81_P	84_N	0.941	0.40
138_N	141_I	0.941	0.40
88_V	124_K	0.928	0.39
3_Y	6_K	0.927	0.39
41_I	70_I	0.924	0.39
69_L	97_G	0.922	0.39
78_H	107_I	0.918	0.39
60_L	100_L	0.904	0.38
5_T	122_P	0.903	0.38
65_K	136_N	0.898	0.37
44_I	48_L	0.895	0.37
91_K	97_G	0.889	0.37
91_K	95_W	0.884	0.37
91_K	106_A	0.849	0.34
73_A	80_I	0.838	0.34
111_Y	118_A	0.837	0.34
110_Y	117_H	0.833	0.34
2_V	120_I	0.829	0.33
7_R	125_S	0.827	0.33
135_K	139_I	0.825	0.33
71_I	103_S	0.824	0.33
39_G	49_L	0.818	0.33
65_K	109_I	0.814	0.32
71_I	78_H	0.811	0.32
100_L	118_A	0.803	0.32
7_R	57_F	0.802	0.32
93_K	96_S	0.800	0.32
53_I	57_F	0.798	0.32
93_K	119_V	0.794	0.31
4_Q	11_V	0.793	0.31
56_S	73_A	0.793	0.31
27_I	56_S	0.793	0.31
12_T	57_F	0.790	0.31
122_P	132_L	0.785	0.31
87_K	117_H	0.783	0.31
93_K	106_A	0.782	0.31
104_R	119_V	0.759	0.29
56_S	134_E	0.758	0.29
94_L	107_I	0.751	0.29
4_Q	57_F	0.741	0.28
57_F	75_L	0.739	0.28
3_Y	135_K	0.738	0.28
3_Y	18_L	0.737	0.28
130_H	134_E	0.731	0.28
93_K	108_T	0.725	0.27
95_W	106_A	0.722	0.27
42_I	72_K	0.721	0.27
76_I	103_S	0.720	0.27
76_I	140_I	0.715	0.27
16_V	52_L	0.712	0.27
65_K	82_Y	0.711	0.27
18_L	58_I	0.711	0.27
5_T	128_F	0.705	0.26
60_L	122_P	0.705	0.26
51_G	75_L	0.704	0.26
15_I	21_L	0.697	0.26
69_L	81_P	0.693	0.26
58_I	88_V	0.692	0.26
8_D	55_W	0.683	0.25
94_L	120_I	0.680	0.25
20_L	43_F	0.679	0.25
8_D	102_G	0.673	0.25
123_Q	132_L	0.672	0.25
14_M	118_A	0.667	0.25
70_I	84_N	0.663	0.24
8_D	103_S	0.662	0.24
7_R	71_I	0.662	0.24
14_M	27_I	0.658	0.24
7_R	96_S	0.652	0.24
70_I	74_G	0.651	0.24
19_I	24_A	0.650	0.24
96_S	120_I	0.645	0.23
23_Q	51_G	0.642	0.23
5_T	8_D	0.639	0.23
63_V	112_Q	0.635	0.23
97_G	101_I	0.633	0.23
42_I	51_G	0.630	0.23
131_K	138_N	0.624	0.22
41_I	118_A	0.620	0.22
101_I	119_V	0.616	0.22
61_K	138_N	0.612	0.22
2_V	7_R	0.612	0.22
68_H	107_I	0.607	0.22
13_L	127_E	0.605	0.22
89_V	110_Y	0.605	0.22
116_G	132_L	0.604	0.22
5_T	96_S	0.603	0.22
7_R	55_W	0.602	0.21
107_I	119_V	0.602	0.21
133_K	139_I	0.598	0.21
13_L	33_G	0.598	0.21
15_I	23_Q	0.598	0.21
2_V	57_F	0.592	0.21
25_D	28_V	0.589	0.21
26_A	109_I	0.589	0.21
101_I	121_S	0.589	0.21
41_I	107_I	0.588	0.21
86_D	136_N	0.588	0.21
57_F	60_L	0.588	0.21
86_D	116_G	0.585	0.21
10_P	97_G	0.583	0.21
71_I	119_V	0.575	0.20
73_A	120_I	0.573	0.20
120_I	123_Q	0.572	0.20
66_E	88_V	0.568	0.20
33_G	70_I	0.564	0.20
70_I	77_K	0.563	0.20
88_V	123_Q	0.561	0.20
61_K	104_R	0.561	0.20
18_L	25_D	0.560	0.20
78_H	119_V	0.558	0.20
121_S	128_F	0.557	0.20
13_L	66_E	0.548	0.19
42_I	88_V	0.543	0.19
55_W	77_K	0.543	0.19
42_I	45_L	0.543	0.19
47_T	67_H	0.542	0.19
58_I	67_H	0.536	0.19
87_K	120_I	0.533	0.19
92_K	105_H	0.530	0.18
56_S	59_D	0.530	0.18
78_H	92_K	0.530	0.18
53_I	73_A	0.517	0.18
58_I	95_W	0.513	0.18
38_S	66_E	0.508	0.18
24_A	45_L	0.505	0.17
62_Y	121_S	0.504	0.17
3_Y	22_I	0.503	0.17
96_S	126_E	0.501	0.17
94_L	101_I	0.500	0.17

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
1vw44	1	0.411	72.8	0.906	Contact Map
5aj3c	1	0.4452	31.5	0.927	Contact Map
1s3aA	1	0.274	26.4	0.93	Contact Map
3j7yb	1	0.4315	16.2	0.937	Contact Map
4e6zA	1	0.2877	14.1	0.938	Contact Map
4tyzA	1	0.726	12.6	0.94	Contact Map
4chmA	1	0.7877	12.6	0.94	Contact Map
2k1aA	1	0.2877	9.3	0.943	Contact Map
2j04B	1	0.3082	6.5	0.947	Contact Map
2kjgA	1	0.5205	5.5	0.949	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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