FliO - PFAM28P - GREMLIN Contacts

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FliO - Flagellar biosynthesis protein, FliO

PFAM:	PF04347	Sequences: WLLRRGFGGGRGGGGGGGGRLRVLARLPLGPRERLVLVEVGGRQLLLGVTPGGITLLHELDDPEEPEPLAAAAAPAPAASFAQLLKRALK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (85)
Sequences:	14917 (12106)
Seq/√Len:	1313.0
META:	0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_R	59_E	3.858	1.00
22_R	39_E	3.167	1.00
21_L	27_L	2.684	1.00
36_V	49_V	2.667	1.00
32_R	51_P	2.447	1.00
26_R	34_R	2.410	1.00
43_R	58_H	2.401	1.00
30_G	33_E	2.043	1.00
48_G	54_I	1.990	1.00
56_L	59_E	1.979	1.00
39_E	44_Q	1.955	1.00
26_R	36_V	1.848	1.00
35_L	38_V	1.842	1.00
84_L	87_R	1.838	1.00
84_L	88_A	1.838	1.00
45_L	58_H	1.799	1.00
50_T	53_G	1.761	1.00
39_E	42_G	1.722	1.00
20_R	25_A	1.665	1.00
49_V	54_I	1.608	1.00
45_L	56_L	1.554	1.00
24_L	39_E	1.541	1.00
82_A	86_K	1.523	1.00
33_E	51_P	1.503	1.00
40_V	46_L	1.492	1.00
37_L	40_V	1.429	1.00
19_G	25_A	1.420	1.00
38_V	47_L	1.358	1.00
41_G	44_Q	1.344	1.00
23_V	27_L	1.319	1.00
24_L	44_Q	1.297	1.00
35_L	46_L	1.258	1.00
29_L	36_V	1.163	1.00
43_R	61_D	1.148	1.00
21_L	37_L	1.144	1.00
1_W	5_R	1.090	1.00
29_L	35_L	1.066	1.00
40_V	60_L	1.064	1.00
33_E	50_T	1.055	1.00
35_L	57_L	1.039	1.00
62_D	65_E	1.005	1.00
34_R	49_V	0.991	1.00
50_T	54_I	0.985	1.00
44_Q	60_L	0.979	1.00
42_G	62_D	0.979	1.00
23_V	36_V	0.957	1.00
62_D	66_P	0.947	1.00
36_V	47_L	0.921	1.00
32_R	36_V	0.895	1.00
27_L	35_L	0.880	1.00
11_R	14_G	0.859	1.00
35_L	54_I	0.855	1.00
26_R	30_G	0.849	1.00
47_L	54_I	0.834	1.00
66_P	69_L	0.821	1.00
72_A	75_P	0.817	1.00
80_S	83_Q	0.802	1.00
23_V	26_R	0.793	1.00
26_R	33_E	0.783	1.00
21_L	40_V	0.781	1.00
83_Q	86_K	0.772	1.00
66_P	70_A	0.772	1.00
33_E	49_V	0.752	1.00
46_L	58_H	0.748	1.00
20_R	41_G	0.739	1.00
44_Q	65_E	0.735	1.00
10_G	13_G	0.733	1.00
63_P	67_E	0.729	1.00
37_L	60_L	0.713	1.00
45_L	59_E	0.712	1.00
65_E	69_L	0.682	1.00
21_L	25_A	0.681	1.00
62_D	69_L	0.677	1.00
63_P	66_P	0.668	1.00
61_D	64_E	0.668	1.00
79_A	83_Q	0.667	1.00
28_P	34_R	0.662	1.00
39_E	70_A	0.658	1.00
72_A	77_P	0.653	1.00
33_E	54_I	0.650	1.00
19_G	27_L	0.649	1.00
44_Q	62_D	0.647	1.00
37_L	46_L	0.633	1.00
82_A	88_A	0.630	1.00
71_A	75_P	0.625	1.00
32_R	37_L	0.621	1.00
46_L	60_L	0.616	1.00
33_E	52_G	0.614	1.00
1_W	4_R	0.611	1.00
11_R	15_G	0.603	1.00
42_G	64_E	0.597	1.00
2_L	5_R	0.593	1.00
30_G	36_V	0.593	1.00
37_L	44_Q	0.589	1.00
39_E	62_D	0.587	1.00
12_G	15_G	0.584	1.00
64_E	68_P	0.583	1.00
75_P	78_A	0.577	1.00
4_R	32_R	0.565	1.00
73_A	76_A	0.561	1.00
25_A	30_G	0.557	1.00
4_R	10_G	0.555	1.00
50_T	55_T	0.554	1.00
48_G	55_T	0.553	1.00
5_R	50_T	0.552	1.00
37_L	45_L	0.547	1.00
44_Q	61_D	0.545	1.00
67_E	70_A	0.545	1.00
20_R	23_V	0.543	1.00
73_A	77_P	0.542	1.00
20_R	44_Q	0.533	1.00
35_L	47_L	0.532	1.00
30_G	49_V	0.531	1.00
65_E	70_A	0.526	1.00
65_E	68_P	0.525	1.00
41_G	65_E	0.525	1.00
31_P	34_R	0.521	1.00
25_A	28_P	0.521	1.00
67_E	71_A	0.519	1.00
73_A	78_A	0.513	1.00
71_A	74_A	0.511	1.00
30_G	34_R	0.510	1.00
4_R	51_P	0.509	1.00
61_D	65_E	0.508	1.00
41_G	60_L	0.506	1.00
81_F	84_L	0.506	1.00
79_A	87_R	0.500	1.00
83_Q	88_A	0.500	1.00

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
3fqmA	2	0.9444	6.2	0.87	Contact Map
4o7oA	2	0.8889	5.3	0.874	Contact Map
4u98A	1	0.9333	3.9	0.882	Contact Map
4gwpC	1	0	3.5	0.885	Contact Map
3e19A	5	0.6111	3.1	0.888	Contact Map
1xrxA	3	0.3778	2.9	0.889	Contact Map
1fx7A	4	0.6222	2.8	0.89	Contact Map
2yweA	1	0	2.8	0.891	Contact Map
2h3gX	2	0.5333	2.6	0.893	Contact Map
3h4lA	2	0.3556	2.5	0.893	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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