Phage_ASH - PFAM28P - GREMLIN Contacts

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Phage_ASH - Ash protein family

PFAM:	PF10554	Sequences: YSFPAPAKSAAGRGNPNLLKATNDAPPAVFFRVVATPHPFFGQWFAIQSMVARAGQPSGWPVSPVAGIANPVRATTPEIGNSGGSSNNLLKEAAIMATTPTTPSHPQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	108 (102)
Sequences:	533 (304)
Seq/√Len:	30.1
META:	0.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_K	91_K	4.321	1.00
19_L	90_L	3.954	1.00
20_K	64_P	3.583	1.00
64_P	91_K	3.402	1.00
14_G	80_G	3.257	1.00
56_Q	60_W	3.083	1.00
6_P	10_A	2.873	1.00
65_V	90_L	2.869	1.00
19_L	65_V	2.674	1.00
78_E	82_S	2.573	1.00
14_G	69_A	2.534	0.99
15_N	68_I	2.496	0.99
53_R	73_R	2.478	0.99
69_A	80_G	2.212	0.98
15_N	81_N	2.101	0.98
61_P	67_G	1.871	0.96
68_I	81_N	1.779	0.94
5_A	11_A	1.753	0.94
94_A	97_A	1.744	0.94
12_G	16_P	1.631	0.91
13_R	79_I	1.609	0.91
57_P	60_W	1.483	0.87
72_V	76_T	1.442	0.85
52_A	74_A	1.408	0.84
55_G	71_P	1.400	0.83
13_R	70_N	1.387	0.83
96_M	99_T	1.295	0.78
78_E	81_N	1.206	0.73
62_V	66_A	1.192	0.72
70_N	79_I	1.192	0.72
54_A	72_V	1.173	0.71
13_R	68_I	1.165	0.70
24_D	27_P	1.112	0.66
65_V	89_L	1.097	0.65
69_A	81_N	1.096	0.65
15_N	69_A	1.096	0.65
15_N	70_N	1.059	0.63
18_L	89_L	1.047	0.62
96_M	100_P	1.017	0.59
56_Q	59_G	1.012	0.59
73_R	76_T	0.999	0.58
19_L	64_P	0.987	0.57
51_V	75_T	0.961	0.55
70_N	76_T	0.951	0.54
70_N	81_N	0.942	0.53
64_P	90_L	0.931	0.53
65_V	91_K	0.906	0.51
15_N	79_I	0.902	0.50
53_R	74_A	0.900	0.50
70_N	75_T	0.897	0.50
14_G	79_I	0.882	0.49
68_I	80_G	0.867	0.48
14_G	81_N	0.859	0.47
18_L	65_V	0.845	0.46
20_K	90_L	0.841	0.45
35_A	38_H	0.838	0.45
42_G	45_F	0.837	0.45
95_I	99_T	0.836	0.45
68_I	79_I	0.834	0.45
69_A	79_I	0.830	0.45
13_R	81_N	0.826	0.44
14_G	68_I	0.800	0.42
74_A	85_S	0.798	0.42
20_K	65_V	0.782	0.41
97_A	100_P	0.782	0.41
1_Y	5_A	0.781	0.41
18_L	66_A	0.772	0.40
15_N	80_G	0.767	0.40
28_A	31_F	0.761	0.39
72_V	75_T	0.759	0.39
52_A	73_R	0.740	0.38
68_I	76_T	0.739	0.38
98_T	102_T	0.736	0.37
99_T	102_T	0.736	0.37
39_P	42_G	0.735	0.37
68_I	71_P	0.727	0.37
96_M	102_T	0.724	0.36
6_P	11_A	0.723	0.36
19_L	66_A	0.714	0.36
7_A	10_A	0.710	0.35
14_G	70_N	0.709	0.35
43_Q	46_A	0.700	0.35
22_T	25_A	0.695	0.34
6_P	9_S	0.693	0.34
66_A	90_L	0.692	0.34
60_W	68_I	0.677	0.33
75_T	84_G	0.670	0.33
95_I	100_P	0.664	0.32
49_S	52_A	0.663	0.32
34_V	38_H	0.645	0.31
41_F	44_W	0.645	0.31
2_S	6_P	0.644	0.31
44_W	48_Q	0.641	0.31
21_A	25_A	0.641	0.31
73_R	85_S	0.635	0.30
33_V	37_P	0.631	0.30
92_E	95_I	0.626	0.30
29_V	32_R	0.626	0.30
13_R	80_G	0.626	0.30
41_F	45_F	0.626	0.30
95_I	98_T	0.623	0.29
29_V	33_V	0.622	0.29
68_I	77_P	0.619	0.29
19_L	91_K	0.614	0.29
95_I	102_T	0.606	0.28
71_P	75_T	0.605	0.28
12_G	67_G	0.603	0.28
13_R	69_A	0.599	0.28
31_F	37_P	0.599	0.28
5_A	10_A	0.595	0.28
36_T	45_F	0.593	0.27
53_R	85_S	0.592	0.27
99_T	104_S	0.592	0.27
36_T	40_F	0.592	0.27
93_A	102_T	0.585	0.27
12_G	15_N	0.580	0.27
35_A	39_P	0.573	0.26
23_N	32_R	0.570	0.26
44_W	47_I	0.570	0.26
49_S	77_P	0.563	0.26
52_A	85_S	0.560	0.25
8_K	21_A	0.558	0.25
40_F	43_Q	0.549	0.25
32_R	38_H	0.547	0.25
65_V	88_N	0.547	0.25
43_Q	47_I	0.547	0.25
49_S	104_S	0.540	0.24
70_N	80_G	0.539	0.24
34_V	39_P	0.535	0.24
3_F	6_P	0.531	0.24
71_P	81_N	0.531	0.24
12_G	61_P	0.529	0.24
18_L	88_N	0.529	0.24
28_A	93_A	0.529	0.24
94_A	98_T	0.527	0.23
31_F	34_V	0.525	0.23
8_K	13_R	0.524	0.23
27_P	31_F	0.524	0.23
73_R	77_P	0.521	0.23
2_S	10_A	0.519	0.23
16_P	67_G	0.518	0.23
29_V	36_T	0.518	0.23
9_S	17_N	0.514	0.23
84_G	94_A	0.514	0.23
13_R	16_P	0.511	0.23
24_D	29_V	0.509	0.22
34_V	40_F	0.508	0.22
94_A	99_T	0.508	0.22
93_A	99_T	0.506	0.22
54_A	57_P	0.504	0.22
25_A	31_F	0.501	0.22
22_T	29_V	0.501	0.22
41_F	46_A	0.500	0.22

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
1lajA	7	0.2222	2.6	0.942	Contact Map
1q38A	1	0.3611	2	0.946	Contact Map
3qwqB	1	0.2407	1.7	0.948	Contact Map
2zy4A	6	0.8796	1.6	0.948	Contact Map
2kbgA	1	0.2963	1.6	0.949	Contact Map
2ee3A	1	0.3333	1.5	0.95	Contact Map
2pc4A	4	0.3148	1.3	0.951	Contact Map
1iarB	1	0.2407	1	0.955	Contact Map
3tgoC	2	0.3148	1	0.955	Contact Map
2b8kG	1	0	1	0.955	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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