Arch_fla_DE - PFAM28P - GREMLIN Contacts

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Arch_fla_DE - Archaeal flagella protein

PFAM:	PF04659	Sequences: EKPYLETLPDDYASEVVVLEWLEFLVERVGREGAADALDYYEDIGWISEDVRDELLDYLRGIDEDDVEKDDWKPSDLTVDDHIQSLLYIAKLAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (91)
Sequences:	632 (442)
Seq/√Len:	46.3
META:	0.775

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_A	59_L	4.424	1.00
22_L	55_L	4.127	1.00
21_W	85_S	3.248	1.00
48_S	51_V	3.202	1.00
9_P	14_S	3.125	1.00
12_Y	15_E	3.026	1.00
40_Y	44_I	2.553	1.00
47_I	51_V	2.346	1.00
25_L	37_A	2.301	1.00
38_L	52_R	2.069	1.00
17_V	92_L	2.009	0.99
29_V	77_L	1.897	0.99
42_E	52_R	1.826	0.99
30_G	33_G	1.571	0.97
77_L	81_D	1.545	0.96
18_V	92_L	1.485	0.95
50_D	54_E	1.476	0.95
59_L	66_D	1.436	0.94
28_R	81_D	1.349	0.92
17_V	31_R	1.317	0.91
89_I	93_A	1.311	0.91
4_Y	93_A	1.301	0.91
23_E	27_E	1.289	0.91
8_L	40_Y	1.235	0.89
29_V	37_A	1.213	0.88
78_T	81_D	1.199	0.87
32_E	69_K	1.188	0.87
51_V	55_L	1.170	0.86
11_D	14_S	1.156	0.85
11_D	15_E	1.153	0.85
43_D	48_S	1.151	0.85
19_L	91_K	1.151	0.85
16_V	20_E	1.145	0.84
33_G	36_D	1.107	0.82
61_G	86_L	1.100	0.82
7_T	50_D	1.082	0.81
33_G	77_L	1.080	0.81
80_D	91_K	1.046	0.79
52_R	71_D	1.007	0.76
22_L	63_D	1.006	0.76
39_D	52_R	0.986	0.74
52_R	56_L	0.951	0.72
62_I	86_L	0.946	0.71
39_D	73_K	0.927	0.70
20_E	88_Y	0.926	0.70
5_L	89_I	0.912	0.68
82_H	85_S	0.902	0.68
40_Y	78_T	0.895	0.67
41_Y	82_H	0.890	0.67
7_T	45_G	0.887	0.66
66_D	71_D	0.884	0.66
56_L	59_L	0.882	0.66
63_D	80_D	0.877	0.65
86_L	90_A	0.864	0.64
27_E	62_I	0.860	0.64
28_R	61_G	0.834	0.61
87_L	90_A	0.833	0.61
82_H	92_L	0.829	0.61
23_E	60_R	0.825	0.61
37_A	59_L	0.822	0.60
33_G	73_K	0.819	0.60
30_G	71_D	0.817	0.60
19_L	84_Q	0.806	0.59
11_D	60_R	0.800	0.58
67_V	70_D	0.800	0.58
8_L	55_L	0.792	0.58
19_L	88_Y	0.789	0.57
21_W	82_H	0.777	0.56
19_L	87_L	0.769	0.55
79_V	90_A	0.767	0.55
35_A	56_L	0.766	0.55
12_Y	18_V	0.746	0.53
74_P	79_V	0.746	0.53
35_A	79_V	0.742	0.53
11_D	16_V	0.742	0.53
87_L	91_K	0.732	0.52
23_E	68_E	0.726	0.51
24_F	80_D	0.720	0.50
85_S	88_Y	0.715	0.50
72_W	75_S	0.714	0.50
17_V	84_Q	0.711	0.50
16_V	67_V	0.695	0.48
12_Y	53_D	0.689	0.47
60_R	76_D	0.678	0.46
31_R	62_I	0.676	0.46
22_L	77_L	0.673	0.46
10_D	60_R	0.668	0.45
38_L	56_L	0.668	0.45
17_V	83_I	0.659	0.44
9_P	71_D	0.653	0.44
58_Y	61_G	0.652	0.44
36_D	81_D	0.647	0.43
70_D	80_D	0.646	0.43
44_I	57_D	0.645	0.43
69_K	72_W	0.641	0.43
13_A	34_A	0.638	0.42
11_D	20_E	0.632	0.42
77_L	83_I	0.631	0.42
40_Y	47_I	0.628	0.41
23_E	86_L	0.627	0.41
39_D	54_E	0.627	0.41
37_A	77_L	0.626	0.41
9_P	20_E	0.622	0.41
28_R	38_L	0.619	0.41
35_A	77_L	0.617	0.40
26_V	30_G	0.613	0.40
49_E	71_D	0.612	0.40
30_G	37_A	0.606	0.39
37_A	92_L	0.605	0.39
66_D	70_D	0.604	0.39
20_E	87_L	0.599	0.39
55_L	70_D	0.598	0.39
49_E	88_Y	0.595	0.38
57_D	68_E	0.594	0.38
16_V	79_V	0.591	0.38
7_T	10_D	0.578	0.37
14_S	20_E	0.576	0.37
84_Q	90_A	0.570	0.36
26_V	77_L	0.566	0.36
41_Y	46_W	0.561	0.35
14_S	91_K	0.559	0.35
88_Y	92_L	0.549	0.34
90_A	93_A	0.541	0.33
45_G	68_E	0.538	0.33
13_A	57_D	0.537	0.33
12_Y	29_V	0.537	0.33
46_W	82_H	0.536	0.33
19_L	92_L	0.531	0.33
24_F	70_D	0.528	0.32
39_D	90_A	0.521	0.32
3_P	80_D	0.514	0.31
56_L	84_Q	0.514	0.31
19_L	61_G	0.512	0.31
17_V	26_V	0.506	0.30
79_V	93_A	0.500	0.30
40_Y	61_G	0.500	0.30

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
2aqeA	1	0.4574	12.6	0.902	Contact Map
2cujA	1	0.4681	12.3	0.903	Contact Map
3mkqA	2	0.4894	8	0.91	Contact Map
1q06A	2	0.5851	6.7	0.913	Contact Map
2fokA	1	0.9787	6.3	0.915	Contact Map
2eljA	1	0.4362	6.1	0.915	Contact Map
2dg6A	2	0.4894	5.5	0.917	Contact Map
3gp4A	4	0.5957	5.4	0.917	Contact Map
3zj0A	1	0.6702	5.2	0.918	Contact Map
1x3uA	1	0.5213	5	0.918	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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