Phage_GPO - PFAM28P - GREMLIN Contacts

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Phage_GPO - Phage capsid scaffolding protein (GPO) serine peptidase

PFAM:	PF05929	Sequences: SKWFRVATEGATTDGREIERQWIEQMAETYDPKTYGARINLEHIRGLLPDSPFGAYGDVLALKAEEVDDGPLEGKLALFAQIEPTDDLVALNKAGQKLYTSIEIDPNFADTGKAYLVGLAVTDSPASLGTEMLKFSAQAKANPLAARKQSPENLFSAAEETELEFEEEPEEEPGASLFARVKALFSKKQKKDDARFADVHQAVEALAEEVAELAEKFAALSALEAELAELKAALAALQADFAALKTKLEKTPASQTQRPPATGGDGAVLTDC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	272 (267)
Sequences:	1149 (855)
Seq/√Len:	52.4
META:	0.42

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_G	99_Y	4.206	1.00
7_A	102_I	3.656	1.00
61_A	81_Q	3.618	1.00
21_Q	25_Q	3.517	1.00
23_I	64_A	3.457	1.00
9_E	20_R	3.387	1.00
29_T	113_K	3.307	1.00
26_M	62_L	3.137	1.00
3_W	63_K	3.134	1.00
107_N	110_D	3.132	1.00
83_E	95_G	2.916	1.00
25_Q	113_K	2.886	1.00
20_R	66_E	2.857	1.00
62_L	80_A	2.739	1.00
240_D	245_K	2.692	1.00
28_E	113_K	2.618	1.00
38_R	58_D	2.613	1.00
109_A	128_L	2.519	1.00
45_R	124_S	2.409	1.00
26_M	104_I	2.381	1.00
25_Q	29_T	2.316	1.00
36_G	98_L	2.286	1.00
39_I	82_I	2.273	1.00
6_V	102_I	2.228	1.00
24_E	28_E	2.176	1.00
67_V	77_A	2.172	1.00
36_G	58_D	2.160	1.00
54_G	87_D	2.153	1.00
226_E	231_K	2.153	1.00
3_W	81_Q	2.096	1.00
40_N	45_R	2.082	1.00
6_V	80_A	2.081	1.00
24_E	76_L	2.080	1.00
233_A	238_Q	2.058	1.00
8_T	77_A	2.035	1.00
23_I	76_L	1.999	1.00
63_K	81_Q	1.969	1.00
5_R	77_A	1.961	1.00
22_W	104_I	1.943	1.00
19_E	22_W	1.934	1.00
58_D	99_Y	1.910	0.99
88_L	121_V	1.902	0.99
30_Y	37_A	1.900	0.99
7_A	18_I	1.838	0.99
85_T	95_G	1.826	0.99
66_E	76_L	1.816	0.99
236_A	240_D	1.794	0.99
40_N	120_A	1.793	0.99
90_A	94_A	1.765	0.99
23_I	26_M	1.743	0.99
69_D	74_G	1.733	0.99
20_R	76_L	1.696	0.99
38_R	55_A	1.695	0.99
241_F	245_K	1.671	0.99
105_D	117_V	1.639	0.98
192_D	195_R	1.628	0.98
98_L	132_M	1.612	0.98
9_E	76_L	1.588	0.98
234_L	237_L	1.524	0.97
237_L	241_F	1.500	0.97
11_A	110_D	1.500	0.97
234_L	241_F	1.489	0.97
188_K	192_D	1.477	0.97
66_E	74_G	1.459	0.96
90_A	93_K	1.453	0.96
20_R	24_E	1.445	0.96
161_T	165_F	1.400	0.96
203_V	206_L	1.387	0.95
121_V	133_L	1.385	0.95
132_M	144_L	1.367	0.95
68_D	74_G	1.340	0.94
64_A	76_L	1.335	0.94
67_V	79_F	1.329	0.94
70_G	74_G	1.322	0.94
209_E	214_A	1.294	0.93
51_S	54_G	1.292	0.93
227_L	230_L	1.290	0.93
5_R	8_T	1.287	0.93
48_L	52_P	1.272	0.93
177_L	181_V	1.256	0.92
58_D	98_L	1.256	0.92
55_A	124_S	1.243	0.92
240_D	243_A	1.238	0.92
234_L	238_Q	1.237	0.92
69_D	73_E	1.209	0.91
8_T	67_V	1.195	0.90
105_D	150_S	1.192	0.90
64_A	79_F	1.184	0.90
31_D	34_T	1.180	0.89
3_W	61_A	1.178	0.89
38_R	99_Y	1.176	0.89
54_G	94_A	1.174	0.89
192_D	196_F	1.165	0.89
199_V	206_L	1.161	0.89
238_Q	242_A	1.154	0.88
100_T	119_L	1.147	0.88
21_Q	24_E	1.115	0.87
245_K	249_E	1.115	0.87
84_P	89_V	1.114	0.87
201_Q	204_E	1.108	0.86
232_A	236_A	1.085	0.85
236_A	239_A	1.083	0.85
34_T	128_L	1.081	0.85
108_F	128_L	1.074	0.84
24_E	64_A	1.069	0.84
107_N	111_T	1.067	0.84
63_K	79_F	1.066	0.84
38_R	98_L	1.066	0.84
149_Q	153_N	1.066	0.84
195_R	200_H	1.052	0.83
235_A	239_A	1.036	0.82
180_R	183_A	1.026	0.82
41_L	91_L	1.024	0.82
243_A	246_T	1.017	0.81
105_D	153_N	1.016	0.81
100_T	161_T	1.011	0.81
55_A	58_D	1.005	0.80
40_N	92_N	0.994	0.80
199_V	203_V	0.993	0.79
7_A	135_F	0.992	0.79
40_N	103_E	0.991	0.79
46_G	53_F	0.991	0.79
100_T	133_L	0.990	0.79
5_R	79_F	0.985	0.79
81_Q	166_E	0.983	0.79
144_L	147_R	0.981	0.79
17_E	107_N	0.976	0.78
18_I	102_I	0.966	0.78
67_V	74_G	0.965	0.78
213_L	216_K	0.956	0.77
34_T	109_A	0.950	0.76
231_K	235_A	0.934	0.75
241_F	249_E	0.934	0.75
48_L	54_G	0.931	0.75
92_N	121_V	0.929	0.75
196_F	199_V	0.925	0.74
24_E	66_E	0.921	0.74
246_T	250_K	0.921	0.74
200_H	206_L	0.918	0.74
103_E	118_G	0.909	0.73
179_A	183_A	0.906	0.73
204_E	208_E	0.900	0.72
196_F	203_V	0.898	0.72
258_R	261_A	0.897	0.72
40_N	55_A	0.895	0.72
223_L	227_L	0.894	0.72
132_M	143_P	0.894	0.72
6_V	62_L	0.893	0.72
87_D	90_A	0.891	0.72
67_V	70_G	0.881	0.71
8_T	75_K	0.880	0.71
202_A	205_A	0.880	0.71
6_V	39_I	0.874	0.70
91_L	121_V	0.869	0.70
230_L	234_L	0.868	0.70
176_S	188_K	0.866	0.69
241_F	244_L	0.859	0.69
183_A	187_K	0.857	0.69
227_L	237_L	0.849	0.68
200_H	203_V	0.845	0.68
107_N	112_G	0.845	0.68
195_R	199_V	0.843	0.67
47_L	50_D	0.836	0.67
104_I	114_A	0.835	0.67
176_S	180_R	0.833	0.66
142_N	145_A	0.831	0.66
69_D	84_P	0.827	0.66
202_A	207_A	0.824	0.66
175_A	180_R	0.823	0.66
6_V	116_L	0.820	0.65
13_T	148_K	0.817	0.65
235_A	238_Q	0.812	0.64
58_D	85_T	0.810	0.64
7_A	55_A	0.810	0.64
30_Y	115_Y	0.809	0.64
208_E	212_E	0.808	0.64
256_T	259_P	0.804	0.64
228_A	231_K	0.804	0.64
229_E	233_A	0.803	0.64
9_E	75_K	0.803	0.64
252_P	255_Q	0.798	0.63
252_P	257_Q	0.795	0.63
59_V	119_L	0.791	0.62
41_L	44_I	0.791	0.62
201_Q	205_A	0.789	0.62
202_A	206_L	0.789	0.62
95_G	132_M	0.788	0.62
41_L	85_T	0.786	0.62
136_S	142_N	0.784	0.62
206_L	209_E	0.782	0.62
265_D	268_V	0.781	0.61
255_Q	259_P	0.778	0.61
253_A	256_T	0.773	0.61
247_K	250_K	0.772	0.61
244_L	247_K	0.766	0.60
2_K	164_E	0.765	0.60
40_N	121_V	0.760	0.59
209_E	213_L	0.756	0.59
82_I	121_V	0.750	0.58
9_E	24_E	0.749	0.58
4_F	82_I	0.748	0.58
144_L	148_K	0.747	0.58
11_A	17_E	0.747	0.58
67_V	73_E	0.746	0.58
42_E	97_K	0.745	0.58
35_Y	130_T	0.741	0.57
37_A	115_Y	0.741	0.57
117_V	153_N	0.741	0.57
92_N	133_L	0.737	0.57
44_I	47_L	0.736	0.57
237_L	240_D	0.735	0.57
190_K	194_A	0.730	0.56
87_D	94_A	0.729	0.56
40_N	117_V	0.727	0.56
256_T	260_P	0.726	0.56
50_D	54_G	0.725	0.56
27_A	30_Y	0.724	0.56
189_Q	192_D	0.723	0.56
198_D	202_A	0.720	0.55
252_P	256_T	0.715	0.55
188_K	195_R	0.714	0.55
208_E	213_L	0.713	0.54
243_A	247_K	0.711	0.54
11_A	107_N	0.705	0.54
5_R	131_E	0.704	0.54
42_E	124_S	0.704	0.54
242_A	246_T	0.703	0.53
97_K	123_D	0.703	0.53
6_V	40_N	0.703	0.53
102_I	106_P	0.701	0.53
249_E	252_P	0.701	0.53
6_V	81_Q	0.700	0.53
29_T	111_T	0.699	0.53
206_L	210_V	0.699	0.53
30_Y	60_L	0.698	0.53
42_E	45_R	0.697	0.53
56_Y	91_L	0.696	0.53
267_A	270_T	0.694	0.53
6_V	100_T	0.693	0.52
70_G	73_E	0.690	0.52
58_D	95_G	0.688	0.52
48_L	51_S	0.686	0.52
34_T	69_D	0.686	0.52
82_I	133_L	0.685	0.52
23_I	27_A	0.682	0.51
195_R	198_D	0.682	0.51
62_L	102_I	0.681	0.51
41_L	49_P	0.681	0.51
67_V	75_K	0.679	0.51
225_A	228_A	0.677	0.51
30_Y	98_L	0.668	0.50
139_A	142_N	0.666	0.50
58_D	132_M	0.666	0.50
111_T	128_L	0.665	0.49
223_L	226_E	0.664	0.49
22_W	25_Q	0.663	0.49
45_R	55_A	0.661	0.49
4_F	89_V	0.656	0.49
181_V	188_K	0.655	0.48
25_Q	114_A	0.654	0.48
19_E	26_M	0.653	0.48
251_T	255_Q	0.653	0.48
30_Y	99_Y	0.652	0.48
196_F	200_H	0.648	0.48
198_D	201_Q	0.648	0.48
224_E	228_A	0.647	0.48
13_T	22_W	0.646	0.47
210_V	214_A	0.644	0.47
4_F	131_E	0.644	0.47
153_N	157_A	0.643	0.47
229_E	232_A	0.642	0.47
140_K	145_A	0.641	0.47
205_A	209_E	0.641	0.47
58_D	83_E	0.640	0.47
174_G	178_F	0.637	0.47
212_E	216_K	0.636	0.46
199_V	202_A	0.634	0.46
23_I	102_I	0.633	0.46
260_P	266_G	0.632	0.46
228_A	232_A	0.631	0.46
80_A	100_T	0.631	0.46
233_A	236_A	0.630	0.46
136_S	144_L	0.629	0.46
26_M	83_E	0.628	0.46
69_D	111_T	0.627	0.45
56_Y	87_D	0.626	0.45
41_L	48_L	0.622	0.45
82_I	119_L	0.620	0.45
8_T	11_A	0.616	0.44
234_L	248_L	0.614	0.44
211_A	214_A	0.614	0.44
236_A	245_K	0.613	0.44
213_L	217_F	0.612	0.44
203_V	210_V	0.604	0.43
36_G	85_T	0.604	0.43
54_G	91_L	0.604	0.43
197_A	262_T	0.603	0.43
54_G	85_T	0.600	0.43
120_A	156_S	0.600	0.43
191_K	195_R	0.597	0.42
39_I	84_P	0.596	0.42
260_P	265_D	0.595	0.42
227_L	234_L	0.595	0.42
55_A	96_Q	0.595	0.42
35_Y	108_F	0.595	0.42
181_V	184_L	0.592	0.42
153_N	160_E	0.591	0.42
26_M	42_E	0.591	0.42
266_G	269_L	0.590	0.42
21_Q	113_K	0.590	0.42
39_I	89_V	0.589	0.42
151_P	154_L	0.589	0.42
246_T	249_E	0.588	0.41
86_D	90_A	0.587	0.41
173_P	176_S	0.585	0.41
148_K	158_A	0.584	0.41
165_F	259_P	0.584	0.41
3_W	22_W	0.583	0.41
8_T	129_G	0.583	0.41
32_P	60_L	0.583	0.41
4_F	20_R	0.582	0.41
134_K	138_Q	0.579	0.41
49_P	53_F	0.579	0.41
5_R	53_F	0.577	0.40
179_A	182_K	0.573	0.40
207_A	210_V	0.572	0.40
100_T	120_A	0.568	0.39
89_V	93_K	0.567	0.39
226_E	234_L	0.564	0.39
178_F	185_F	0.564	0.39
264_G	268_V	0.562	0.39
46_G	52_P	0.560	0.39
225_A	247_K	0.560	0.39
60_L	83_E	0.559	0.39
193_D	200_H	0.558	0.38
177_L	182_K	0.557	0.38
47_L	51_S	0.557	0.38
131_E	156_S	0.556	0.38
22_W	105_D	0.554	0.38
108_F	115_Y	0.553	0.38
89_V	92_N	0.553	0.38
8_T	33_K	0.553	0.38
203_V	207_A	0.551	0.38
75_K	128_L	0.550	0.38
62_L	113_K	0.549	0.38
237_L	244_L	0.547	0.37
62_L	99_Y	0.546	0.37
5_R	67_V	0.544	0.37
260_P	268_V	0.542	0.37
41_L	56_Y	0.539	0.37
148_K	154_L	0.536	0.36
11_A	22_W	0.536	0.36
7_A	26_M	0.535	0.36
232_A	235_A	0.534	0.36
98_L	136_S	0.533	0.36
227_L	231_K	0.533	0.36
255_Q	269_L	0.532	0.36
85_T	89_V	0.531	0.36
203_V	211_A	0.531	0.36
226_E	233_A	0.530	0.36
198_D	203_V	0.529	0.36
105_D	152_E	0.529	0.36
211_A	217_F	0.528	0.36
75_K	109_A	0.526	0.35
41_L	55_A	0.525	0.35
147_R	153_N	0.525	0.35
86_D	93_K	0.524	0.35
37_A	59_V	0.524	0.35
197_A	200_H	0.522	0.35
231_K	241_F	0.521	0.35
10_G	14_D	0.521	0.35
205_A	208_E	0.521	0.35
40_N	124_S	0.520	0.35
256_T	268_V	0.519	0.35
222_A	227_L	0.518	0.35
45_R	106_P	0.518	0.35
41_L	121_V	0.518	0.35
145_A	148_K	0.516	0.34
233_A	246_T	0.515	0.34
15_G	148_K	0.514	0.34
150_S	153_N	0.514	0.34
50_D	53_F	0.513	0.34
147_R	151_P	0.513	0.34
239_A	242_A	0.512	0.34
27_A	62_L	0.512	0.34
180_R	184_L	0.511	0.34
167_E	173_P	0.509	0.34
210_V	216_K	0.509	0.34
22_W	26_M	0.509	0.34
87_D	91_L	0.509	0.34
191_K	202_A	0.507	0.34
22_W	106_P	0.504	0.33
28_E	64_A	0.504	0.33
13_T	16_R	0.503	0.33
176_S	179_A	0.502	0.33
190_K	269_L	0.502	0.33
34_T	108_F	0.502	0.33
249_E	255_Q	0.501	0.33
9_E	66_E	0.501	0.33
186_S	190_K	0.500	0.33

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
4r3zA	1	0.2574	39.5	0.96	Contact Map
1fzcC	2	0.2096	38.8	0.961	Contact Map
3qprA	8	0.0037	34.6	0.962	Contact Map
2yy0A	6	0.1949	32.9	0.962	Contact Map
4dznA	3	0.1176	22.7	0.965	Contact Map
1lwuC	1	0.2647	22.1	0.965	Contact Map
4rsiA	1	0.2537	19.3	0.966	Contact Map
1lwuB	1	0.2537	18.2	0.966	Contact Map
1fzcB	1	0.2169	15.9	0.967	Contact Map
4emcA	2	0.2794	15.6	0.967	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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