NKWYS - PFAM28P - GREMLIN Contacts

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NKWYS - Putative capsular polysaccharide synthesis protein

PFAM:	PF10364	Sequences: IEGKKNDDIEIDSEKTLELLEEFFLEYFPHDYPLDWFDRELKPVFGIDVYAHPFDKEKGYQIYENGNVDLLLLRLEDLDRLEEAIGEFLGLPDFKLVNANVGSEKWYADLYREFKERIRLPEEYLDRMYSSKYARHFYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (121)
Sequences:	1287 (1176)
Seq/√Len:	106.9
META:	0.93

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_R	77_D	4.060	1.00
76_E	138_Y	3.950	1.00
64_E	69_D	3.431	1.00
102_G	107_Y	3.375	1.00
38_D	42_K	3.128	1.00
52_H	63_Y	2.682	1.00
47_I	70_L	2.640	1.00
41_L	70_L	2.581	1.00
34_L	131_S	2.449	1.00
77_D	80_R	2.308	1.00
100_N	105_K	2.056	1.00
48_D	51_A	2.044	1.00
38_D	132_K	1.994	1.00
31_D	127_R	1.803	1.00
81_L	84_A	1.751	1.00
71_L	88_F	1.684	1.00
125_L	129_Y	1.684	1.00
113_E	117_R	1.625	1.00
62_I	69_D	1.575	1.00
82_E	95_K	1.554	1.00
79_D	98_N	1.483	1.00
23_F	27_Y	1.481	1.00
45_F	68_V	1.456	1.00
98_N	101_V	1.454	1.00
56_K	139_S	1.449	1.00
20_L	23_F	1.431	1.00
124_Y	128_M	1.416	1.00
50_Y	136_H	1.412	1.00
22_E	26_E	1.408	1.00
85_I	94_F	1.367	1.00
25_L	28_F	1.360	1.00
41_L	45_F	1.329	0.99
55_D	58_K	1.301	0.99
19_L	25_L	1.296	0.99
50_Y	133_Y	1.290	0.99
47_I	65_N	1.274	0.99
122_E	126_D	1.266	0.99
24_F	27_Y	1.261	0.99
54_F	59_G	1.254	0.99
130_S	135_R	1.252	0.99
40_E	44_V	1.228	0.99
71_L	84_A	1.221	0.99
131_S	134_A	1.220	0.99
82_E	94_F	1.201	0.99
126_D	130_S	1.178	0.99
19_L	23_F	1.149	0.98
102_G	105_K	1.149	0.98
76_E	129_Y	1.098	0.98
34_L	128_M	1.095	0.98
53_P	136_H	1.094	0.98
42_K	48_D	1.091	0.98
83_E	87_E	1.061	0.97
65_N	68_V	1.044	0.97
24_F	28_F	1.025	0.97
113_E	116_E	1.024	0.97
101_V	104_E	0.994	0.96
102_G	111_Y	0.985	0.96
114_F	124_Y	0.985	0.96
75_L	78_L	0.971	0.96
101_V	105_K	0.969	0.96
59_G	77_D	0.965	0.95
112_R	115_K	0.959	0.95
50_Y	132_K	0.958	0.95
55_D	61_Q	0.955	0.95
19_L	24_F	0.953	0.95
40_E	43_P	0.951	0.95
35_D	39_R	0.938	0.95
30_H	124_Y	0.933	0.94
118_I	121_P	0.928	0.94
120_L	124_Y	0.914	0.94
86_G	92_P	0.913	0.94
75_L	102_G	0.903	0.93
73_L	79_D	0.903	0.93
49_V	72_L	0.902	0.93
73_L	81_L	0.895	0.93
30_H	128_M	0.894	0.93
73_L	84_A	0.892	0.93
103_S	112_R	0.877	0.92
50_Y	137_F	0.876	0.92
21_E	25_L	0.871	0.92
77_D	81_L	0.870	0.92
129_Y	134_A	0.866	0.92
78_L	81_L	0.863	0.92
36_W	41_L	0.840	0.91
128_M	134_A	0.835	0.90
86_G	91_L	0.831	0.90
63_Y	72_L	0.818	0.90
122_E	125_L	0.813	0.89
121_P	124_Y	0.812	0.89
60_Y	81_L	0.804	0.89
114_F	138_Y	0.803	0.89
19_L	27_Y	0.799	0.88
96_L	99_A	0.798	0.88
69_D	88_F	0.793	0.88
134_A	138_Y	0.793	0.88
82_E	93_D	0.781	0.87
60_Y	87_E	0.781	0.87
37_F	49_V	0.775	0.87
50_Y	131_S	0.765	0.86
28_F	32_Y	0.763	0.86
52_H	65_N	0.757	0.86
22_E	25_L	0.755	0.85
23_F	28_F	0.753	0.85
63_Y	70_L	0.752	0.85
111_Y	129_Y	0.749	0.85
53_P	135_R	0.745	0.85
19_L	22_E	0.741	0.84
52_H	61_Q	0.739	0.84
102_G	108_A	0.737	0.84
75_L	81_L	0.730	0.84
23_F	26_E	0.722	0.83
78_L	129_Y	0.721	0.83
77_D	138_Y	0.713	0.82
59_G	76_E	0.705	0.81
126_D	129_Y	0.701	0.81
37_F	40_E	0.680	0.79
54_F	57_E	0.679	0.79
109_D	113_E	0.667	0.78
60_Y	84_A	0.666	0.78
76_E	84_A	0.664	0.77
58_K	87_E	0.650	0.76
85_I	89_L	0.649	0.76
81_L	86_G	0.646	0.75
65_N	69_D	0.644	0.75
45_F	81_L	0.642	0.75
55_D	59_G	0.637	0.74
106_W	117_R	0.633	0.74
54_F	137_F	0.629	0.73
62_I	88_F	0.626	0.73
21_E	118_I	0.626	0.73
107_Y	111_Y	0.622	0.73
25_L	121_P	0.619	0.72
43_P	53_P	0.618	0.72
91_L	94_F	0.617	0.72
79_D	96_L	0.615	0.72
77_D	129_Y	0.614	0.72
96_L	100_N	0.608	0.71
131_S	137_F	0.607	0.71
83_E	86_G	0.606	0.71
95_K	123_E	0.605	0.71
53_P	57_E	0.605	0.71
33_P	113_E	0.604	0.70
74_R	138_Y	0.597	0.70
20_L	27_Y	0.597	0.70
40_E	45_F	0.595	0.69
41_L	44_V	0.595	0.69
38_D	50_Y	0.594	0.69
86_G	94_F	0.591	0.69
108_A	115_K	0.584	0.68
49_V	136_H	0.583	0.68
49_V	89_L	0.581	0.67
77_D	84_A	0.578	0.67
48_D	136_H	0.578	0.67
54_F	63_Y	0.576	0.67
58_K	130_S	0.570	0.66
39_R	43_P	0.569	0.66
59_G	74_R	0.566	0.65
37_F	102_G	0.566	0.65
68_V	129_Y	0.563	0.65
22_E	83_E	0.560	0.65
24_F	30_H	0.558	0.64
118_I	124_Y	0.549	0.63
129_Y	139_S	0.549	0.63
20_L	24_F	0.543	0.62
57_E	112_R	0.530	0.60
78_L	96_L	0.530	0.60
66_G	69_D	0.529	0.60
41_L	133_Y	0.528	0.60
52_H	98_N	0.522	0.59
56_K	74_R	0.521	0.59
73_L	120_L	0.519	0.59
35_D	56_K	0.519	0.59
86_G	93_D	0.518	0.59
86_G	89_L	0.515	0.58
30_H	33_P	0.512	0.58
80_R	119_R	0.510	0.58
40_E	47_I	0.507	0.57
71_L	85_I	0.507	0.57
58_K	135_R	0.506	0.57
92_P	95_K	0.504	0.57
75_L	79_D	0.503	0.57
33_P	124_Y	0.500	0.56

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
3mcrA	2	0.3885	8.9	0.932	Contact Map
1nu0A	1	0.6547	4.2	0.941	Contact Map
4gdfA	2	0.446	4	0.942	Contact Map
1ghhA	1	0.2446	3.7	0.943	Contact Map
1vhxA	2	0.6619	3.1	0.945	Contact Map
1texA	2	0.7266	3	0.946	Contact Map
1iv0A	1	0.6187	2.6	0.947	Contact Map
3tr4A	5	0.7842	2.1	0.95	Contact Map
1sxvA	5	0.7914	2.1	0.95	Contact Map
4j1jD	3	0.4173	1.9	0.951	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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