FliX - PFAM28P - GREMLIN Contacts

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FliX - Class II flagellar assembly regulator

PFAM:	PF10768	Sequences: MRIYGPNGTAAASAARAARRAGGGGFSLPLEAAAAAAAAAAAAPRAVGGIDALLALQGVEEDPTERRRRAVRRGRDLLDALDELKLGLLSGTLPPATLARLAAAVAELRESSGDPGLDAVLDEIELRAAVELAKLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (133)
Sequences:	2589 (1837)
Seq/√Len:	159.3
META:	0.925

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
125_E	129_A	3.882	1.00
112_S	118_D	3.388	1.00
82_D	85_K	2.986	1.00
109_R	122_D	2.857	1.00
86_L	90_S	2.766	1.00
126_L	129_A	2.725	1.00
77_L	128_A	2.510	1.00
113_G	118_D	2.508	1.00
80_A	83_E	2.325	1.00
87_G	97_T	2.314	1.00
119_A	123_E	2.153	1.00
13_S	16_R	2.054	1.00
74_G	124_I	1.996	1.00
80_A	100_R	1.977	1.00
77_L	105_V	1.921	1.00
95_P	99_A	1.920	1.00
103_A	107_E	1.860	1.00
97_T	100_R	1.801	1.00
68_R	71_V	1.780	1.00
83_E	97_T	1.727	1.00
99_A	103_A	1.701	1.00
67_R	71_V	1.698	1.00
6_P	9_T	1.646	1.00
55_A	58_G	1.618	1.00
109_R	125_E	1.577	1.00
122_D	126_L	1.558	1.00
70_A	121_L	1.539	1.00
74_G	121_L	1.518	1.00
106_A	129_A	1.492	1.00
100_R	103_A	1.489	1.00
103_A	106_A	1.472	1.00
60_E	65_E	1.465	1.00
8_G	11_A	1.458	1.00
83_E	100_R	1.395	1.00
85_K	123_E	1.392	1.00
18_A	21_A	1.382	1.00
93_L	98_L	1.369	1.00
14_A	17_A	1.363	1.00
116_G	120_V	1.351	1.00
54_L	57_Q	1.345	1.00
131_E	134_K	1.330	1.00
120_V	123_E	1.297	1.00
76_D	104_A	1.274	1.00
83_E	87_G	1.267	1.00
119_A	122_D	1.263	1.00
41_A	44_P	1.263	1.00
105_V	122_D	1.238	1.00
125_E	134_K	1.219	1.00
62_D	65_E	1.210	1.00
102_A	106_A	1.205	1.00
9_T	12_A	1.173	1.00
121_L	125_E	1.173	1.00
93_L	97_T	1.167	1.00
63_P	66_R	1.165	1.00
77_L	80_A	1.162	1.00
46_A	49_G	1.134	1.00
87_G	132_L	1.112	1.00
82_D	86_L	1.076	0.99
130_V	133_A	1.069	0.99
130_V	134_K	1.063	0.99
127_R	131_E	1.054	0.99
16_R	19_R	1.044	0.99
93_L	135_L	1.039	0.99
15_A	21_A	1.037	0.99
80_A	97_T	1.037	0.99
127_R	130_V	1.027	0.99
94_P	97_T	1.003	0.99
102_A	129_A	1.001	0.99
4_Y	8_G	1.000	0.99
87_G	90_S	0.990	0.99
105_V	109_R	0.988	0.99
2_R	7_N	0.983	0.99
51_D	56_L	0.981	0.99
4_Y	7_N	0.971	0.99
12_A	15_A	0.969	0.99
22_G	92_T	0.959	0.99
87_G	93_L	0.957	0.99
118_D	122_D	0.951	0.99
80_A	84_L	0.950	0.99
118_D	126_L	0.939	0.98
82_D	134_K	0.939	0.98
125_E	128_A	0.933	0.98
105_V	108_L	0.932	0.98
105_V	121_L	0.931	0.98
13_S	18_A	0.924	0.98
28_L	32_A	0.923	0.98
73_R	110_E	0.920	0.98
49_G	58_G	0.917	0.98
75_R	79_D	0.910	0.98
126_L	130_V	0.909	0.98
75_R	86_L	0.882	0.98
74_G	77_L	0.865	0.97
71_V	120_V	0.858	0.97
73_R	77_L	0.853	0.97
29_P	32_A	0.815	0.96
94_P	135_L	0.810	0.96
29_P	36_A	0.808	0.96
73_R	109_R	0.803	0.96
82_D	90_S	0.799	0.96
23_G	27_S	0.798	0.96
17_A	21_A	0.796	0.96
100_R	107_E	0.796	0.96
67_R	134_K	0.793	0.96
47_V	51_D	0.788	0.95
128_A	132_L	0.778	0.95
84_L	92_T	0.774	0.95
14_A	19_R	0.766	0.95
60_E	63_P	0.764	0.95
67_R	112_S	0.763	0.95
132_L	135_L	0.759	0.94
59_V	74_G	0.750	0.94
22_G	29_P	0.749	0.94
7_N	10_A	0.738	0.94
73_R	107_E	0.735	0.93
18_A	22_G	0.733	0.93
10_A	29_P	0.727	0.93
51_D	54_L	0.711	0.92
80_A	101_L	0.710	0.92
76_D	107_E	0.709	0.92
2_R	6_P	0.708	0.92
10_A	15_A	0.706	0.92
13_S	17_A	0.706	0.92
75_R	80_A	0.704	0.92
62_D	66_R	0.703	0.92
101_L	128_A	0.698	0.92
71_V	134_K	0.694	0.91
58_G	62_D	0.686	0.91
3_I	80_A	0.682	0.91
11_A	15_A	0.681	0.91
102_A	105_V	0.676	0.90
92_T	135_L	0.675	0.90
9_T	33_A	0.672	0.90
1_M	4_Y	0.669	0.90
85_K	89_L	0.669	0.90
77_L	108_L	0.658	0.89
34_A	52_A	0.648	0.88
76_D	97_T	0.628	0.87
104_A	107_E	0.628	0.87
76_D	83_E	0.628	0.87
69_R	110_E	0.616	0.86
72_R	75_R	0.614	0.86
123_E	134_K	0.613	0.85
65_E	68_R	0.613	0.85
73_R	106_A	0.612	0.85
67_R	113_G	0.605	0.85
53_L	56_L	0.599	0.84
5_G	10_A	0.596	0.84
52_A	58_G	0.595	0.84
114_D	120_V	0.590	0.83
10_A	13_S	0.589	0.83
3_I	54_L	0.585	0.83
122_D	125_E	0.585	0.83
84_L	87_G	0.579	0.82
52_A	70_A	0.578	0.82
85_K	134_K	0.578	0.82
14_A	20_R	0.574	0.81
38_A	73_R	0.574	0.81
29_P	99_A	0.570	0.81
14_A	18_A	0.567	0.81
63_P	85_K	0.563	0.80
63_P	67_R	0.562	0.80
108_L	118_D	0.562	0.80
31_E	43_A	0.560	0.80
79_D	82_D	0.559	0.80
21_A	39_A	0.558	0.80
62_D	69_R	0.556	0.79
98_L	135_L	0.555	0.79
19_R	22_G	0.554	0.79
40_A	111_S	0.550	0.79
102_A	122_D	0.548	0.78
4_Y	10_A	0.544	0.78
32_A	66_R	0.544	0.78
87_G	94_P	0.542	0.78
109_R	128_A	0.538	0.77
39_A	104_A	0.538	0.77
28_L	56_L	0.537	0.77
37_A	40_A	0.533	0.77
67_R	85_K	0.530	0.76
50_I	95_P	0.528	0.76
129_A	135_L	0.527	0.76
11_A	18_A	0.527	0.76
62_D	68_R	0.526	0.76
8_G	132_L	0.525	0.75
55_A	85_K	0.523	0.75
12_A	19_R	0.521	0.75
127_R	133_A	0.520	0.75
99_A	102_A	0.520	0.75
108_L	128_A	0.517	0.74
78_L	123_E	0.515	0.74
59_V	62_D	0.515	0.74
60_E	69_R	0.513	0.74
2_R	8_G	0.512	0.74
20_R	23_G	0.510	0.73
31_E	115_P	0.510	0.73
42_A	45_R	0.507	0.73
12_A	41_A	0.506	0.73
46_A	68_R	0.503	0.72
41_A	47_V	0.502	0.72
69_R	125_E	0.501	0.72
32_A	41_A	0.500	0.72

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
4errA	2	0.5735	16.4	0.913	Contact Map
1zl8A	1	0.3897	12.8	0.917	Contact Map
1e6yB	2	0.3676	9.2	0.922	Contact Map
2y1nA	1	0.4632	7.1	0.926	Contact Map
1hbnB	2	0.3897	5.3	0.93	Contact Map
3sqgB	2	0.3603	4.8	0.931	Contact Map
3iqtA	1	0.7279	4.3	0.933	Contact Map
2rbdA	4	0.3309	3.7	0.935	Contact Map
2a0bA	1	0.6765	3.6	0.935	Contact Map
2d9dA	1	0.5074	3.6	0.936	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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