Phage_lysis - PFAM28P - GREMLIN Contacts

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Phage_lysis - Bacteriophage Rz lysis protein

PFAM:	PF03245	Sequences: NAITYKDQRDKATAALAQANAEIDKRQARQRDLAALDAKHTKELADAKAEIDRLRDDLATGDLRLRVKATCPAGVPATTGAGGVDDAARARLDPAAAQDYFAIRDRGDTALIQLRALQAYIREQCL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (118)
Sequences:	1971 (1243)
Seq/√Len:	114.4
META:	0.438

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_I	26_R	3.067	1.00
42_K	46_D	2.903	1.00
37_D	41_T	2.510	1.00
110_A	114_L	2.427	1.00
16_L	19_A	2.230	1.00
85_D	116_A	2.197	1.00
119_A	123_E	2.190	1.00
57_D	63_L	2.183	1.00
114_L	117_L	2.061	1.00
107_G	111_L	2.059	1.00
110_A	113_Q	2.040	1.00
16_L	20_N	1.932	1.00
47_A	50_E	1.867	1.00
12_A	15_A	1.835	1.00
23_I	27_Q	1.801	1.00
57_D	62_D	1.796	1.00
91_R	97_A	1.771	1.00
93_D	107_G	1.743	1.00
8_Q	12_A	1.682	1.00
9_R	13_T	1.657	1.00
82_G	116_A	1.605	1.00
11_K	15_A	1.601	1.00
58_L	61_G	1.584	1.00
15_A	19_A	1.542	1.00
115_R	118_Q	1.540	1.00
8_Q	11_K	1.521	1.00
117_L	121_I	1.519	1.00
107_G	110_A	1.479	1.00
104_R	107_G	1.472	1.00
95_A	106_R	1.452	1.00
38_A	42_K	1.450	1.00
9_R	12_A	1.442	1.00
8_Q	13_T	1.437	1.00
111_L	114_L	1.437	1.00
7_D	11_K	1.406	1.00
22_E	26_R	1.392	1.00
39_K	43_E	1.374	1.00
25_K	29_R	1.363	1.00
49_A	53_R	1.361	1.00
26_R	29_R	1.325	1.00
111_L	115_R	1.308	1.00
103_I	106_R	1.307	1.00
53_R	57_D	1.297	1.00
56_D	60_T	1.284	0.99
57_D	64_R	1.275	0.99
97_A	100_Y	1.273	0.99
40_H	44_L	1.272	0.99
48_K	52_D	1.269	0.99
14_A	17_A	1.218	0.99
100_Y	103_I	1.213	0.99
24_D	28_A	1.190	0.99
83_G	86_D	1.180	0.99
26_R	30_Q	1.134	0.99
58_L	101_F	1.132	0.99
53_R	56_D	1.118	0.99
106_R	110_A	1.103	0.98
11_K	14_A	1.084	0.98
50_E	53_R	1.050	0.98
24_D	27_Q	1.037	0.98
17_A	21_A	1.036	0.98
120_Y	124_Q	1.035	0.98
12_A	16_L	1.010	0.97
118_Q	121_I	0.995	0.97
99_D	103_I	0.965	0.96
55_R	59_A	0.960	0.96
13_T	17_A	0.948	0.96
115_R	119_A	0.946	0.96
10_D	13_T	0.942	0.96
13_T	20_N	0.938	0.96
65_L	101_F	0.929	0.95
97_A	101_F	0.924	0.95
41_T	44_L	0.921	0.95
36_L	40_H	0.920	0.95
52_D	55_R	0.917	0.95
100_Y	104_R	0.917	0.95
91_R	94_P	0.910	0.95
63_L	66_R	0.909	0.95
41_T	45_A	0.890	0.94
7_D	10_D	0.888	0.94
100_Y	108_D	0.887	0.94
108_D	111_L	0.881	0.94
17_A	20_N	0.878	0.94
109_T	112_I	0.864	0.93
12_A	17_A	0.862	0.93
15_A	18_Q	0.858	0.93
105_D	109_T	0.843	0.92
21_A	24_D	0.837	0.92
117_L	120_Y	0.809	0.91
98_Q	106_R	0.803	0.90
46_D	50_E	0.802	0.90
34_A	37_D	0.802	0.90
112_I	115_R	0.791	0.90
95_A	98_Q	0.791	0.90
51_I	55_R	0.784	0.89
37_D	44_L	0.780	0.89
93_D	96_A	0.779	0.89
41_T	87_A	0.776	0.89
106_R	109_T	0.773	0.89
15_A	20_N	0.769	0.88
34_A	38_A	0.767	0.88
109_T	113_Q	0.759	0.88
102_A	106_R	0.752	0.87
9_R	14_A	0.739	0.86
36_L	41_T	0.738	0.86
12_A	19_A	0.734	0.86
95_A	107_G	0.731	0.86
7_D	13_T	0.729	0.86
22_E	25_K	0.728	0.85
14_A	18_Q	0.727	0.85
13_T	19_A	0.709	0.84
68_K	71_C	0.698	0.83
7_D	14_A	0.695	0.83
54_L	58_L	0.695	0.83
114_L	121_I	0.690	0.82
104_R	108_D	0.689	0.82
21_A	25_K	0.683	0.82
78_T	84_V	0.676	0.81
113_Q	116_A	0.672	0.81
94_P	97_A	0.670	0.80
25_K	28_A	0.669	0.80
62_D	65_L	0.666	0.80
102_A	105_D	0.665	0.80
44_L	48_K	0.653	0.79
93_D	111_L	0.651	0.78
92_L	100_Y	0.648	0.78
110_A	115_R	0.646	0.78
10_D	15_A	0.646	0.78
19_A	29_R	0.645	0.78
10_D	14_A	0.641	0.77
20_N	23_I	0.635	0.77
71_C	74_G	0.633	0.76
96_A	100_Y	0.631	0.76
90_A	97_A	0.628	0.76
9_R	15_A	0.625	0.76
23_I	29_R	0.614	0.74
114_L	118_Q	0.610	0.74
97_A	106_R	0.607	0.73
48_K	109_T	0.605	0.73
103_I	107_G	0.601	0.73
119_A	124_Q	0.601	0.73
45_A	49_A	0.597	0.72
90_A	110_A	0.586	0.71
70_T	73_A	0.585	0.71
7_D	12_A	0.575	0.69
95_A	103_I	0.570	0.69
13_T	16_L	0.567	0.68
7_D	15_A	0.567	0.68
13_T	28_A	0.565	0.68
95_A	99_D	0.558	0.67
58_L	102_A	0.558	0.67
118_Q	122_R	0.556	0.67
103_I	114_L	0.552	0.66
8_Q	31_R	0.552	0.66
10_D	19_A	0.551	0.66
32_D	35_A	0.550	0.66
87_A	113_Q	0.549	0.66
35_A	38_A	0.549	0.66
100_Y	113_Q	0.549	0.66
103_I	110_A	0.546	0.65
8_Q	20_N	0.544	0.65
49_A	52_D	0.544	0.65
22_E	27_Q	0.544	0.65
11_K	17_A	0.542	0.65
40_H	43_E	0.532	0.63
93_D	97_A	0.531	0.63
106_R	111_L	0.530	0.63
59_A	98_Q	0.528	0.63
89_R	115_R	0.528	0.63
51_I	54_L	0.527	0.63
19_A	22_E	0.523	0.62
85_D	114_L	0.518	0.61
81_A	120_Y	0.518	0.61
91_R	96_A	0.517	0.61
59_A	66_R	0.514	0.61
60_T	78_T	0.504	0.59
43_E	46_D	0.503	0.59
84_V	87_A	0.500	0.59

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
2bnxA	2	0.0873	25.3	0.888	Contact Map
4cgkA	3	0.9762	19.6	0.894	Contact Map
4q4gX	1	0	19	0.894	Contact Map
4rsjA	2	0.4603	14.7	0.9	Contact Map
3sggA	1	0.2937	13.2	0.902	Contact Map
3mq7A	6	0.5238	7.8	0.912	Contact Map
2msvA	1	0.2619	7.7	0.912	Contact Map
3ojaB	1	0.4683	7.4	0.913	Contact Map
1gaxA	1	0.4921	7.3	0.913	Contact Map
1lwuA	2	0.3492	6.7	0.914	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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