YWIB - BACSU - GREMLIN Contacts

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YWIB - Uncharacterized beta-barrel protein YwiB

UniProt:	O07624	Sequences: MKQETPITLHVKSVIEDDGNQEVIEFRTTGFYYVKQNKVYLSYYEEHDLGKVKTIVKVSEGEVLVMRSGAVKMNQRFVTGASTIAKYKMSFGELELKTSTKSIQSDLDEEKGRISIAYDMHVGDEQEHLHNMTITYEGGTHA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	142 (133)
Sequences:	743 (651)
Seq/√Len:	56.5

BACSU - YWIB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_I	66_M	3.584	1.00
78_V	81_A	3.385	1.00
56_V	65_V	3.243	1.00
40_Y	57_K	3.172	1.00
82_S	97_K	3.076	1.00
44_Y	53_K	3.050	1.00
35_K	40_Y	2.881	1.00
32_Y	39_V	2.454	1.00
105_S	114_I	2.334	1.00
82_S	99_S	2.197	1.00
107_L	112_G	2.178	1.00
63_V	116_I	2.054	1.00
12_K	133_T	1.916	1.00
67_R	112_G	1.751	0.99
33_Y	40_Y	1.740	0.99
41_L	136_Y	1.720	0.99
97_K	121_H	1.710	0.99
41_L	58_V	1.698	0.99
115_S	133_T	1.685	0.99
100_T	103_I	1.676	0.99
77_F	100_T	1.670	0.99
11_V	134_I	1.661	0.99
13_S	130_H	1.638	0.99
77_F	116_I	1.626	0.99
11_V	43_Y	1.625	0.99
9_L	30_G	1.609	0.99
101_K	119_D	1.520	0.98
12_K	25_E	1.509	0.98
54_T	67_R	1.497	0.98
75_Q	98_T	1.486	0.98
113_R	135_T	1.469	0.97
46_E	51_K	1.461	0.97
120_M	127_E	1.453	0.97
15_I	130_H	1.445	0.97
14_V	23_V	1.393	0.96
116_I	132_M	1.383	0.96
62_E	78_V	1.378	0.96
78_V	83_T	1.353	0.96
117_A	131_N	1.318	0.95
72_K	88_K	1.269	0.94
112_G	136_Y	1.266	0.94
108_D	111_K	1.254	0.93
100_T	116_I	1.227	0.93
10_H	27_R	1.214	0.92
59_S	62_E	1.210	0.92
64_L	74_N	1.205	0.92
28_T	46_E	1.197	0.92
36_Q	40_Y	1.186	0.91
34_V	39_V	1.184	0.91
5_T	33_Y	1.158	0.90
35_K	57_K	1.150	0.90
102_S	117_A	1.142	0.90
119_D	129_L	1.142	0.90
104_Q	113_R	1.132	0.89
17_D	20_N	1.130	0.89
13_S	24_I	1.125	0.89
63_V	92_G	1.123	0.89
120_M	130_H	1.122	0.89
34_V	109_E	1.117	0.89
120_M	128_H	1.104	0.88
38_K	59_S	1.093	0.88
34_V	61_G	1.088	0.87
48_D	52_V	1.079	0.87
54_T	132_M	1.076	0.87
96_L	122_V	1.074	0.87
7_I	41_L	1.069	0.86
24_I	103_I	1.066	0.86
102_S	115_S	1.053	0.86
33_Y	57_K	1.037	0.85
9_L	82_S	1.034	0.85
105_S	136_Y	1.008	0.83
122_V	127_E	1.007	0.83
34_V	37_N	0.968	0.80
43_Y	92_G	0.960	0.80
45_E	67_R	0.956	0.80
35_K	38_K	0.955	0.80
77_F	85_A	0.946	0.79
96_L	124_D	0.942	0.79
58_V	92_G	0.937	0.78
14_V	21_Q	0.934	0.78
29_T	46_E	0.930	0.78
73_M	98_T	0.929	0.78
85_A	98_T	0.919	0.77
101_K	117_A	0.908	0.76
96_L	121_H	0.903	0.76
77_F	118_Y	0.897	0.75
45_E	69_G	0.888	0.74
41_L	56_V	0.870	0.73
63_V	103_I	0.868	0.73
22_E	128_H	0.867	0.73
64_L	128_H	0.863	0.72
16_E	114_I	0.850	0.71
13_S	128_H	0.844	0.71
51_K	70_A	0.838	0.70
112_G	130_H	0.833	0.70
18_D	137_E	0.830	0.69
105_S	112_G	0.817	0.68
48_D	51_K	0.806	0.67
42_S	53_K	0.797	0.66
61_G	78_V	0.795	0.66
16_E	94_L	0.794	0.66
87_Y	118_Y	0.793	0.66
22_E	45_E	0.787	0.65
33_Y	42_S	0.782	0.65
47_H	52_V	0.776	0.64
21_Q	94_L	0.775	0.64
8_T	137_E	0.770	0.63
7_I	110_E	0.766	0.63
50_G	91_F	0.762	0.63
46_E	49_L	0.760	0.62
15_I	94_L	0.759	0.62
52_V	71_V	0.751	0.61
79_T	102_S	0.738	0.60
84_I	97_K	0.732	0.60
43_Y	75_Q	0.724	0.59
89_M	132_M	0.724	0.59
7_I	26_F	0.718	0.58
14_V	103_I	0.715	0.58
8_T	52_V	0.712	0.57
11_V	30_G	0.708	0.57
20_N	63_V	0.701	0.56
58_V	63_V	0.699	0.56
106_D	113_R	0.683	0.54
71_V	136_Y	0.678	0.54
8_T	29_T	0.675	0.53
32_Y	48_D	0.666	0.52
68_S	72_K	0.660	0.52
57_K	105_S	0.652	0.51
85_A	116_I	0.651	0.51
58_V	111_K	0.650	0.51
49_L	70_A	0.649	0.51
48_D	65_V	0.646	0.50
41_L	132_M	0.642	0.50
38_K	60_E	0.642	0.50
93_E	108_D	0.638	0.49
91_F	104_Q	0.637	0.49
94_L	98_T	0.633	0.49
94_L	103_I	0.628	0.48
104_Q	108_D	0.621	0.48
62_E	76_R	0.620	0.47
104_Q	109_E	0.617	0.47
14_V	131_N	0.610	0.46
52_V	70_A	0.608	0.46
63_V	114_I	0.607	0.46
6_P	29_T	0.605	0.46
13_S	136_Y	0.605	0.46
37_N	60_E	0.604	0.46
75_Q	92_G	0.602	0.45
46_E	50_G	0.600	0.45
123_G	132_M	0.600	0.45
89_M	92_G	0.600	0.45
13_S	91_F	0.599	0.45
64_L	76_R	0.597	0.45
10_H	135_T	0.596	0.45
42_S	55_I	0.595	0.45
33_Y	36_Q	0.594	0.45
85_A	128_H	0.592	0.44
10_H	96_L	0.591	0.44
101_K	129_L	0.591	0.44
94_L	127_E	0.590	0.44
7_I	111_K	0.582	0.43
22_E	84_I	0.582	0.43
39_V	111_K	0.577	0.43
8_T	48_D	0.577	0.43
88_K	93_E	0.576	0.43
74_N	123_G	0.575	0.43
28_T	43_Y	0.574	0.42
54_T	64_L	0.573	0.42
13_S	98_T	0.573	0.42
35_K	66_M	0.568	0.42
72_K	120_M	0.568	0.42
71_V	93_E	0.567	0.42
67_R	130_H	0.558	0.41
87_Y	91_F	0.554	0.40
5_T	13_S	0.553	0.40
63_V	68_S	0.552	0.40
65_V	137_E	0.549	0.40
95_E	99_S	0.549	0.40
43_Y	107_L	0.547	0.40
121_H	125_E	0.547	0.40
75_Q	110_E	0.539	0.39
61_G	79_T	0.537	0.39
66_M	127_E	0.534	0.38
58_V	105_S	0.534	0.38
28_T	112_G	0.534	0.38
30_G	55_I	0.534	0.38
15_I	68_S	0.529	0.38
37_N	101_K	0.524	0.37
78_V	82_S	0.524	0.37
12_K	23_V	0.519	0.37
15_I	82_S	0.516	0.36
50_G	80_G	0.516	0.36
64_L	112_G	0.513	0.36
84_I	94_L	0.510	0.36
76_R	84_I	0.508	0.36
24_I	130_H	0.507	0.36
58_V	114_I	0.506	0.35
54_T	91_F	0.506	0.35
52_V	82_S	0.501	0.35
25_E	98_T	0.500	0.35

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
1r0uA	1	0.9577	100	0.116	Contact Map
3mx7A	1	0.6338	7.4	0.936	Contact Map
2c1lA	2	0.7535	4.2	0.943	Contact Map
4a60A	1	0.7042	4.1	0.943	Contact Map
3zigA	2	0.4225	3.7	0.944	Contact Map
3wbgA	1	0.7113	3.7	0.945	Contact Map
1kmtA	1	0.7958	3.6	0.945	Contact Map
4aznA	1	0.7113	3.6	0.945	Contact Map
4l3aA	1	0.8732	3.5	0.945	Contact Map
3fyfA	2	0.8521	3.3	0.946	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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