Phage_X - PFAM28P - GREMLIN Contacts

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Phage_X - Phage X family

PFAM:	PF05155	Sequences: LTSEGIVSLTKAANATAFYYLLWMHGYDLRKLLSKSTFYRHRARLLEIGIDIAQLQNLSKFSNVVPLVRVIEVDPAQIPDWYQEPVSM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	88 (84)
Sequences:	783 (554)
Seq/√Len:	60.4
META:	0.727

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_T	40_R	4.184	1.00
36_S	43_A	3.542	1.00
42_R	53_A	2.981	1.00
36_S	40_R	2.643	1.00
7_V	12_A	2.362	1.00
43_A	47_E	2.182	1.00
8_S	11_K	2.181	1.00
44_R	47_E	2.160	1.00
42_R	46_L	2.126	1.00
10_T	14_N	2.067	1.00
35_K	39_Y	1.996	1.00
42_R	52_I	1.945	1.00
34_S	40_R	1.933	1.00
11_K	14_N	1.869	1.00
34_S	37_T	1.787	0.99
64_V	69_R	1.766	0.99
11_K	15_A	1.640	0.99
37_T	41_H	1.549	0.98
31_K	35_K	1.543	0.98
30_R	35_K	1.450	0.98
58_L	61_F	1.422	0.97
23_W	52_I	1.353	0.96
66_P	69_R	1.341	0.96
20_Y	23_W	1.301	0.96
46_L	52_I	1.228	0.94
17_A	21_L	1.221	0.94
37_T	44_R	1.212	0.93
4_E	8_S	1.181	0.93
78_I	84_E	1.156	0.92
82_Y	85_P	1.150	0.92
22_L	25_H	1.147	0.91
54_Q	57_N	1.134	0.91
20_Y	50_I	1.131	0.91
9_L	13_A	1.126	0.91
22_L	27_Y	1.096	0.89
65_V	69_R	1.036	0.87
18_F	22_L	1.007	0.85
16_T	41_H	1.002	0.85
42_R	51_D	0.984	0.84
3_S	7_V	0.981	0.84
57_N	60_K	0.979	0.83
46_L	53_A	0.972	0.83
18_F	41_H	0.966	0.83
30_R	38_F	0.952	0.82
17_A	20_Y	0.944	0.81
6_I	10_T	0.939	0.81
23_W	42_R	0.920	0.79
33_L	41_H	0.917	0.79
6_I	9_L	0.916	0.79
40_R	44_R	0.904	0.78
60_K	71_I	0.884	0.77
13_A	44_R	0.865	0.75
49_G	85_P	0.863	0.75
35_K	42_R	0.850	0.74
61_F	65_V	0.846	0.73
68_V	74_D	0.844	0.73
27_Y	56_Q	0.831	0.72
15_A	44_R	0.830	0.72
45_L	49_G	0.825	0.71
56_Q	65_V	0.819	0.71
9_L	12_A	0.803	0.69
14_N	67_L	0.800	0.69
68_V	73_V	0.798	0.69
29_L	38_F	0.797	0.69
13_A	48_I	0.795	0.69
10_T	18_F	0.784	0.68
12_A	44_R	0.782	0.67
67_L	73_V	0.778	0.67
46_L	51_D	0.749	0.64
21_L	24_M	0.748	0.64
40_R	43_A	0.746	0.64
12_A	50_I	0.743	0.63
58_L	62_S	0.727	0.62
70_V	78_I	0.709	0.60
13_A	16_T	0.704	0.59
53_A	56_Q	0.703	0.59
43_A	46_L	0.699	0.59
63_N	83_Q	0.696	0.58
68_V	76_A	0.665	0.55
50_I	60_K	0.663	0.55
63_N	66_P	0.662	0.55
62_S	72_E	0.657	0.54
19_Y	38_F	0.644	0.53
41_H	82_Y	0.642	0.52
16_T	29_L	0.639	0.52
44_R	48_I	0.637	0.52
56_Q	67_L	0.633	0.51
39_Y	43_A	0.617	0.50
74_D	78_I	0.608	0.49
21_L	25_H	0.606	0.48
3_S	66_P	0.601	0.48
69_R	72_E	0.600	0.48
23_W	51_D	0.599	0.48
20_Y	63_N	0.598	0.47
37_T	43_A	0.597	0.47
3_S	6_I	0.596	0.47
7_V	11_K	0.593	0.47
16_T	65_V	0.590	0.46
3_S	8_S	0.576	0.45
68_V	72_E	0.574	0.45
7_V	13_A	0.571	0.44
36_S	39_Y	0.571	0.44
34_S	44_R	0.568	0.44
80_D	86_V	0.567	0.44
49_G	58_L	0.559	0.43
43_A	59_S	0.556	0.43
28_D	69_R	0.552	0.42
10_T	17_A	0.542	0.41
6_I	17_A	0.541	0.41
56_Q	59_S	0.536	0.41
77_Q	80_D	0.536	0.41
4_E	7_V	0.536	0.41
81_W	84_E	0.531	0.40
63_N	67_L	0.531	0.40
57_N	68_V	0.529	0.40
5_G	8_S	0.521	0.39
73_V	76_A	0.519	0.39
26_G	50_I	0.518	0.39
45_L	57_N	0.516	0.38
19_Y	43_A	0.515	0.38
38_F	53_A	0.512	0.38
12_A	31_K	0.511	0.38
14_N	21_L	0.509	0.38
17_A	41_H	0.509	0.38
80_D	84_E	0.506	0.37
19_Y	34_S	0.500	0.37

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
4cwcA	2	0.8068	92.6	0.812	Contact Map
3a8gA	1	0.9886	35.7	0.886	Contact Map
3qyhA	1	0.9773	31.2	0.889	Contact Map
3hhtA	1	0.9886	29.5	0.891	Contact Map
4ob1A	1	0.9886	24.2	0.895	Contact Map
4ob0A	1	0.9886	19	0.9	Contact Map
4zgjA	2	0.9659	17.6	0.902	Contact Map
3iuoA	4	0.9545	10.3	0.911	Contact Map
3ke2A	2	0.7955	9	0.913	Contact Map
2fu4A	2	0.7159	7.7	0.916	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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