17kDa_Anti_2 - PFAM28P - GREMLIN Contacts

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17kDa_Anti_2 - 17 kDa outer membrane surface antigen

PFAM:	PF16998	Sequences: GGFDLDGAFKMDDSDVTGSIAAAAAAASPTESDLAFARAAASDALTRGGKDASVPWENPDTGARGTVTPLASAYQDGRTCRDFLASYVRGGGESWLQGEACRQGDGRWEVRSLKPW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (103)
Sequences:	2286 (1405)
Seq/√Len:	138.5
META:	0.906

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_R	104_G	3.478	1.00
33_D	58_N	2.770	1.00
44_A	54_V	2.677	1.00
88_V	93_E	2.472	1.00
58_N	61_T	2.453	1.00
57_E	64_R	2.352	1.00
84_L	95_W	2.340	1.00
82_D	97_Q	2.179	1.00
43_D	47_R	2.119	1.00
22_A	25_A	2.041	1.00
16_V	19_S	2.015	1.00
25_A	29_P	1.875	1.00
83_F	98_G	1.841	1.00
35_A	39_A	1.838	1.00
27_A	31_E	1.760	1.00
99_E	111_R	1.752	1.00
30_T	33_D	1.702	1.00
39_A	43_D	1.680	1.00
78_R	103_Q	1.654	1.00
13_D	16_V	1.550	1.00
34_L	37_A	1.547	1.00
34_L	41_A	1.515	1.00
17_T	20_I	1.446	1.00
25_A	28_S	1.441	1.00
53_S	68_T	1.440	1.00
83_F	100_A	1.439	1.00
64_R	88_V	1.430	1.00
31_E	35_A	1.419	1.00
84_L	97_Q	1.406	1.00
48_G	51_D	1.319	1.00
89_R	94_S	1.304	1.00
36_F	67_V	1.294	1.00
31_E	34_L	1.285	1.00
71_A	82_D	1.284	1.00
28_S	31_E	1.280	1.00
15_D	20_I	1.272	1.00
86_S	93_E	1.272	1.00
29_P	32_S	1.258	1.00
65_G	87_Y	1.247	1.00
46_T	50_K	1.222	1.00
22_A	26_A	1.220	1.00
70_L	84_L	1.211	1.00
87_Y	91_G	1.143	0.99
33_D	40_A	1.139	0.99
15_D	19_S	1.124	0.99
14_S	20_I	1.114	0.99
46_T	70_L	1.105	0.99
36_F	39_A	1.098	0.99
36_F	43_D	1.081	0.99
50_K	72_S	1.075	0.99
81_R	108_W	1.063	0.99
48_G	54_V	1.059	0.99
26_A	29_P	1.054	0.99
63_A	87_Y	1.052	0.99
32_S	36_F	1.026	0.99
43_D	48_G	1.018	0.99
86_S	95_W	0.997	0.98
13_D	21_A	0.987	0.98
67_V	86_S	0.984	0.98
19_S	22_A	0.974	0.98
32_S	92_G	0.968	0.98
17_T	21_A	0.967	0.98
37_A	41_A	0.949	0.98
33_D	37_A	0.932	0.97
30_T	34_L	0.921	0.97
58_N	62_G	0.920	0.97
36_F	40_A	0.914	0.97
64_R	93_E	0.902	0.97
103_Q	109_E	0.895	0.97
66_T	88_V	0.894	0.97
32_S	35_A	0.891	0.97
27_A	30_T	0.887	0.97
55_P	95_W	0.882	0.96
51_D	69_P	0.869	0.96
35_A	38_R	0.864	0.96
74_Y	82_D	0.854	0.96
30_T	60_D	0.842	0.95
20_I	92_G	0.813	0.94
46_T	51_D	0.812	0.94
16_V	20_I	0.810	0.94
34_L	38_R	0.810	0.94
58_N	85_A	0.809	0.94
23_A	27_A	0.804	0.94
72_S	79_T	0.781	0.93
43_D	46_T	0.779	0.93
55_P	66_T	0.770	0.93
74_Y	79_T	0.770	0.93
39_A	42_S	0.769	0.93
13_D	19_S	0.768	0.92
16_V	21_A	0.757	0.92
40_A	57_E	0.733	0.91
84_L	88_V	0.727	0.90
101_C	108_W	0.702	0.89
63_A	89_R	0.686	0.88
87_Y	96_L	0.684	0.87
45_L	49_G	0.682	0.87
53_S	67_V	0.662	0.86
63_A	86_S	0.662	0.86
66_T	99_E	0.653	0.85
18_G	21_A	0.653	0.85
66_T	96_L	0.653	0.85
65_G	86_S	0.650	0.85
89_R	92_G	0.636	0.83
103_Q	107_R	0.634	0.83
20_I	115_P	0.632	0.83
23_A	52_A	0.624	0.82
53_S	66_T	0.618	0.82
56_W	80_C	0.615	0.81
80_C	101_C	0.613	0.81
70_L	76_D	0.609	0.81
40_A	45_L	0.601	0.80
23_A	26_A	0.600	0.80
85_A	96_L	0.595	0.79
26_A	75_Q	0.592	0.79
83_F	110_V	0.589	0.78
45_L	48_G	0.584	0.78
60_D	105_D	0.581	0.77
29_P	61_T	0.579	0.77
47_R	51_D	0.579	0.77
18_G	24_A	0.579	0.77
73_A	79_T	0.575	0.77
112_S	115_P	0.565	0.75
59_P	69_P	0.563	0.75
38_R	76_D	0.558	0.75
78_R	110_V	0.556	0.74
91_G	114_K	0.555	0.74
99_E	103_Q	0.555	0.74
74_Y	84_L	0.553	0.74
71_A	76_D	0.552	0.74
54_V	112_S	0.550	0.74
37_A	40_A	0.548	0.73
86_S	89_R	0.546	0.73
24_A	27_A	0.543	0.73
13_D	52_A	0.540	0.72
13_D	60_D	0.539	0.72
72_S	75_Q	0.539	0.72
111_R	114_K	0.538	0.72
66_T	70_L	0.535	0.72
22_A	28_S	0.534	0.71
76_D	84_L	0.532	0.71
71_A	84_L	0.532	0.71
46_T	49_G	0.530	0.71
69_P	100_A	0.530	0.71
13_D	31_E	0.525	0.70
38_R	42_S	0.524	0.70
29_P	33_D	0.521	0.70
58_N	83_F	0.515	0.69
39_A	54_V	0.514	0.68
50_K	70_L	0.513	0.68
79_T	102_R	0.507	0.67
29_P	37_A	0.507	0.67
54_V	70_L	0.503	0.67
13_D	18_G	0.501	0.67
74_Y	85_A	0.500	0.66

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
4pd2A	1	0.8707	6	0.922	Contact Map
2hbpA	1	0.4224	5.4	0.924	Contact Map
2a2lA	5	0.3448	5.1	0.925	Contact Map
1k82A	1	0.8017	4.3	0.927	Contact Map
1o0eA	1	0.4397	4.3	0.928	Contact Map
1yalA	2	0.4397	4.1	0.928	Contact Map
4clcA	5	0.3707	4.1	0.928	Contact Map
3u6pA	1	0.7155	4.1	0.928	Contact Map
2xu3A	1	0.4397	3.9	0.929	Contact Map
3kwzA	1	0.4397	3.9	0.929	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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