Peptidase_U4 - PFAM28P - GREMLIN Contacts

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Peptidase_U4 - Sporulation factor SpoIIGA

PFAM:	PF03419	Sequences: VVYLDVLFLLNFLMDYLLLLLTAKLLKRKVKRWRLLLGALLGALYAVLLLFLPGLSSFLYSLLLKLLVSLLMVLIAFGPKSLKRFLKLLLVFYLVSFLLGGALLALHYLFLQPSGWLFLLLGAAIAYILIKLVFRLIKRRKRKKDLLYEVEITLGGKSVELKALLDTGNQLRDPLTGKPVIIVEYEALKELLPEELRELLEESEEDDLDEILEELLDSEWASRLRLIPYRSVGGENGLLLGFKPDKVEIEGEGEKIEIKKVLIGISPGKLSKDGEYQALLHPEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	284 (277)
Sequences:	2512 (2213)
Seq/√Len:	133.0
META:	0.715

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_G	76_A	4.637	1.00
153_T	246_K	4.401	1.00
148_Y	165_L	4.192	1.00
41_L	75_I	3.861	1.00
149_E	162_K	3.687	1.00
241_G	262_L	3.564	1.00
42_G	72_M	3.549	1.00
151_E	248_E	3.306	1.00
69_S	93_Y	3.134	1.00
151_E	160_E	3.005	1.00
151_E	158_S	2.957	1.00
246_K	257_E	2.824	1.00
163_A	278_A	2.719	1.00
231_S	234_G	2.693	1.00
150_V	181_I	2.667	1.00
247_V	261_V	2.533	1.00
16_Y	39_A	2.459	1.00
185_Y	267_P	2.434	1.00
149_E	160_E	2.394	1.00
181_I	247_V	2.386	1.00
161_L	187_A	2.353	1.00
229_Y	237_G	2.313	1.00
241_G	264_G	2.308	1.00
16_Y	32_R	2.291	1.00
152_I	244_P	2.262	1.00
38_G	72_M	2.193	1.00
227_I	241_G	2.184	1.00
153_T	156_G	2.183	1.00
147_L	162_K	2.181	1.00
12_F	43_A	2.137	1.00
173_D	262_L	2.128	1.00
25_L	95_V	2.045	1.00
38_G	75_I	2.028	1.00
244_P	263_I	2.008	1.00
161_L	183_V	2.001	1.00
153_T	158_S	1.996	1.00
23_A	30_V	1.993	1.00
172_R	281_H	1.960	1.00
239_L	264_G	1.916	1.00
26_L	88_L	1.915	1.00
19_L	35_L	1.908	1.00
182_I	239_L	1.883	1.00
184_E	277_Q	1.826	1.00
28_R	84_R	1.805	1.00
183_V	188_L	1.779	1.00
173_D	225_R	1.766	1.00
97_F	105_A	1.703	1.00
149_E	250_E	1.695	1.00
151_E	250_E	1.687	1.00
23_A	77_F	1.670	1.00
229_Y	233_G	1.649	1.00
164_L	279_L	1.638	1.00
89_L	93_Y	1.635	1.00
248_E	255_K	1.611	1.00
72_M	92_F	1.603	1.00
150_V	278_A	1.584	1.00
206_D	210_E	1.558	1.00
228_P	238_L	1.554	1.00
154_L	242_F	1.522	1.00
231_S	237_G	1.511	1.00
152_I	161_L	1.503	1.00
172_R	283_E	1.495	1.00
173_D	241_G	1.488	1.00
8_F	43_A	1.484	1.00
161_L	278_A	1.442	1.00
220_W	223_R	1.437	1.00
26_L	91_V	1.428	1.00
173_D	176_T	1.424	1.00
12_F	15_D	1.418	1.00
18_L	92_F	1.415	1.00
70_L	85_F	1.415	1.00
178_K	260_K	1.386	1.00
152_I	183_V	1.378	1.00
65_K	92_F	1.376	1.00
150_V	163_A	1.364	1.00
152_I	247_V	1.362	1.00
65_K	69_S	1.355	1.00
2_V	7_L	1.348	1.00
16_Y	35_L	1.328	1.00
12_F	36_L	1.312	1.00
193_P	196_L	1.292	1.00
186_E	189_K	1.288	1.00
226_L	238_L	1.278	1.00
184_E	270_L	1.269	1.00
14_M	18_L	1.252	1.00
28_R	88_L	1.248	1.00
122_G	127_Y	1.238	1.00
148_Y	280_L	1.201	1.00
5_D	10_L	1.190	0.99
22_T	92_F	1.185	0.99
271_S	276_Y	1.183	0.99
194_E	198_E	1.179	0.99
85_F	89_L	1.162	0.99
224_L	242_F	1.144	0.99
233_G	237_G	1.142	0.99
96_S	100_G	1.136	0.99
6_V	10_L	1.126	0.99
207_D	210_E	1.125	0.99
205_E	208_L	1.118	0.99
70_L	89_L	1.118	0.99
171_L	229_Y	1.113	0.99
45_Y	68_V	1.106	0.99
185_Y	197_R	1.100	0.99
242_F	265_I	1.096	0.99
185_Y	189_K	1.093	0.99
174_P	228_P	1.079	0.99
42_G	92_F	1.065	0.99
187_A	277_Q	1.063	0.99
181_I	278_A	1.062	0.99
22_T	77_F	1.059	0.99
127_Y	131_K	1.057	0.99
18_L	95_V	1.056	0.99
174_P	227_I	1.054	0.99
43_A	53_P	1.037	0.99
148_Y	164_L	1.035	0.99
178_K	243_K	1.029	0.98
171_L	182_I	1.025	0.98
172_R	177_G	1.023	0.98
181_I	261_V	1.016	0.98
116_W	123_A	1.012	0.98
103_L	107_H	1.010	0.98
65_K	104_L	1.008	0.98
240_L	265_I	0.999	0.98
5_D	228_P	0.995	0.98
209_D	212_L	0.990	0.98
20_L	35_L	0.986	0.98
22_T	91_V	0.977	0.98
269_K	274_G	0.976	0.98
176_T	225_R	0.976	0.98
19_L	72_M	0.975	0.98
12_F	16_Y	0.972	0.98
215_L	218_S	0.969	0.98
124_A	128_I	0.964	0.98
10_L	119_L	0.954	0.97
32_R	36_L	0.948	0.97
208_L	212_L	0.946	0.97
93_Y	97_F	0.941	0.97
102_A	105_A	0.941	0.97
102_A	126_A	0.938	0.97
98_L	102_A	0.937	0.97
86_L	90_L	0.934	0.97
105_A	109_L	0.933	0.97
184_E	269_K	0.928	0.97
206_D	209_D	0.927	0.97
128_I	132_L	0.920	0.97
69_S	92_F	0.919	0.97
62_L	116_W	0.914	0.97
11_N	46_A	0.913	0.97
182_I	232_V	0.908	0.97
22_T	95_V	0.907	0.97
68_V	72_M	0.905	0.97
127_Y	130_I	0.905	0.97
81_S	84_R	0.903	0.96
155_G	223_R	0.898	0.96
15_D	42_G	0.895	0.96
95_V	99_L	0.895	0.96
111_L	115_G	0.889	0.96
131_K	135_R	0.885	0.96
208_L	211_I	0.883	0.96
79_P	85_F	0.879	0.96
243_K	260_K	0.875	0.96
223_R	245_D	0.875	0.96
118_F	167_T	0.873	0.96
118_F	123_A	0.873	0.96
83_K	87_K	0.872	0.96
207_D	211_I	0.869	0.96
65_K	96_S	0.867	0.96
104_L	108_Y	0.865	0.95
258_I	261_V	0.865	0.95
84_R	88_L	0.851	0.95
15_D	72_M	0.846	0.95
69_S	73_V	0.845	0.95
30_V	76_A	0.841	0.95
34_R	78_G	0.836	0.95
232_V	266_S	0.835	0.95
74_L	85_F	0.834	0.94
118_F	122_G	0.833	0.94
10_L	18_L	0.832	0.94
102_A	106_L	0.824	0.94
12_F	40_L	0.822	0.94
230_R	235_E	0.818	0.94
77_F	228_P	0.814	0.94
210_E	213_E	0.814	0.94
183_V	263_I	0.813	0.94
123_A	127_Y	0.808	0.94
17_L	123_A	0.805	0.93
23_A	29_K	0.803	0.93
92_F	96_S	0.796	0.93
176_T	262_L	0.794	0.93
244_P	278_A	0.793	0.93
96_S	119_L	0.790	0.93
18_L	96_S	0.782	0.92
229_Y	234_G	0.782	0.92
228_P	241_G	0.781	0.92
250_E	255_K	0.779	0.92
250_E	253_G	0.778	0.92
2_V	6_V	0.775	0.92
175_L	225_R	0.771	0.92
181_I	244_P	0.769	0.92
47_V	53_P	0.766	0.92
248_E	257_E	0.764	0.91
65_K	93_Y	0.762	0.91
229_Y	232_V	0.762	0.91
180_V	227_I	0.758	0.91
209_D	213_E	0.750	0.91
77_F	88_L	0.748	0.91
207_D	213_E	0.748	0.91
67_L	253_G	0.746	0.91
156_G	245_D	0.745	0.90
94_L	102_A	0.744	0.90
157_K	191_L	0.744	0.90
163_A	280_L	0.741	0.90
189_K	197_R	0.740	0.90
73_V	89_L	0.739	0.90
174_P	241_G	0.738	0.90
247_V	258_I	0.736	0.90
9_L	13_L	0.736	0.90
185_Y	192_L	0.735	0.90
153_T	248_E	0.734	0.90
278_A	281_H	0.732	0.90
118_F	131_K	0.732	0.90
182_I	276_Y	0.729	0.89
118_F	127_Y	0.727	0.89
208_L	213_E	0.725	0.89
242_F	263_I	0.725	0.89
41_L	71_L	0.725	0.89
19_L	76_A	0.721	0.89
17_L	127_Y	0.721	0.89
217_D	221_A	0.717	0.89
270_L	274_G	0.717	0.89
6_V	9_L	0.717	0.89
143_K	146_L	0.716	0.89
45_Y	92_F	0.712	0.88
8_F	47_V	0.710	0.88
243_K	262_L	0.709	0.88
169_N	280_L	0.708	0.88
239_L	276_Y	0.708	0.88
8_F	12_F	0.707	0.88
180_V	232_V	0.704	0.88
150_V	249_I	0.704	0.88
38_G	42_G	0.704	0.88
232_V	237_G	0.703	0.88
164_L	276_Y	0.703	0.88
225_R	243_K	0.695	0.87
154_L	245_D	0.692	0.87
216_L	219_E	0.692	0.87
45_Y	65_K	0.690	0.87
2_V	5_D	0.686	0.86
24_K	28_R	0.685	0.86
233_G	266_S	0.682	0.86
92_F	105_A	0.681	0.86
148_Y	249_I	0.681	0.86
16_Y	20_L	0.681	0.86
186_E	269_K	0.681	0.86
227_I	262_L	0.678	0.86
134_F	137_I	0.675	0.86
209_D	216_L	0.675	0.86
165_L	244_P	0.672	0.85
159_V	190_E	0.672	0.85
205_E	212_L	0.671	0.85
184_E	229_Y	0.671	0.85
80_K	84_R	0.670	0.85
178_K	242_F	0.670	0.85
205_E	210_E	0.670	0.85
2_V	46_A	0.668	0.85
205_E	213_E	0.660	0.84
234_G	237_G	0.659	0.84
175_L	262_L	0.658	0.84
117_L	120_L	0.658	0.84
30_V	35_L	0.658	0.84
17_L	48_L	0.654	0.84
167_T	170_Q	0.653	0.84
21_L	95_V	0.653	0.84
206_D	213_E	0.648	0.83
223_R	243_K	0.648	0.83
39_A	42_G	0.648	0.83
183_V	278_A	0.647	0.83
78_G	88_L	0.646	0.83
213_E	216_L	0.645	0.83
65_K	105_A	0.643	0.83
246_K	259_K	0.643	0.83
73_V	93_Y	0.640	0.82
215_L	279_L	0.640	0.82
10_L	96_S	0.639	0.82
169_N	281_H	0.638	0.82
155_G	219_E	0.638	0.82
162_K	277_Q	0.634	0.82
178_K	225_R	0.630	0.81
123_A	130_I	0.627	0.81
130_I	167_T	0.627	0.81
251_G	254_E	0.627	0.81
124_A	127_Y	0.626	0.81
19_L	42_G	0.625	0.81
184_E	274_G	0.625	0.81
185_Y	200_L	0.622	0.81
23_A	76_A	0.622	0.81
156_G	273_D	0.621	0.81
175_L	226_L	0.621	0.81
18_L	99_L	0.620	0.80
205_E	209_D	0.619	0.80
156_G	159_V	0.617	0.80
56_S	59_L	0.616	0.80
271_S	274_G	0.615	0.80
116_W	119_L	0.613	0.80
240_L	244_P	0.612	0.80
121_L	124_A	0.610	0.79
90_L	94_L	0.610	0.79
15_D	43_A	0.609	0.79
66_L	73_V	0.607	0.79
171_L	237_G	0.604	0.79
159_V	191_L	0.602	0.78
147_L	164_L	0.600	0.78
15_D	93_Y	0.600	0.78
119_L	122_G	0.600	0.78
50_L	60_Y	0.600	0.78
195_E	217_D	0.596	0.78
61_S	64_L	0.595	0.78
10_L	14_M	0.595	0.78
179_P	280_L	0.595	0.78
79_P	88_L	0.595	0.78
46_A	72_M	0.593	0.77
211_I	214_E	0.592	0.77
116_W	127_Y	0.591	0.77
126_A	129_L	0.589	0.77
99_L	126_A	0.588	0.77
179_P	261_V	0.586	0.77
261_V	264_G	0.586	0.77
16_Y	121_L	0.583	0.76
100_G	133_V	0.583	0.76
214_E	217_D	0.583	0.76
8_F	15_D	0.581	0.76
195_E	198_E	0.580	0.76
19_L	38_G	0.579	0.76
209_D	214_E	0.577	0.75
226_L	240_L	0.573	0.75
206_D	212_L	0.572	0.75
152_I	263_I	0.571	0.75
39_A	92_F	0.571	0.75
197_R	215_L	0.570	0.75
45_Y	59_L	0.570	0.75
12_F	39_A	0.570	0.75
152_I	278_A	0.569	0.74
232_V	239_L	0.568	0.74
42_G	45_Y	0.568	0.74
108_Y	152_I	0.566	0.74
32_R	82_L	0.565	0.74
211_I	216_L	0.564	0.74
94_L	255_K	0.563	0.74
210_E	214_E	0.563	0.74
244_P	247_V	0.561	0.73
165_L	279_L	0.561	0.73
65_K	72_M	0.559	0.73
84_R	87_K	0.557	0.73
11_N	14_M	0.555	0.73
256_I	259_K	0.554	0.73
50_L	53_P	0.554	0.73
45_Y	100_G	0.553	0.72
172_R	179_P	0.552	0.72
154_L	192_L	0.552	0.72
28_R	32_R	0.551	0.72
188_L	265_I	0.550	0.72
124_A	130_I	0.549	0.72
116_W	128_I	0.546	0.71
129_L	133_V	0.546	0.71
235_E	268_G	0.546	0.71
154_L	244_P	0.544	0.71
186_E	277_Q	0.544	0.71
150_V	161_L	0.544	0.71
51_F	60_Y	0.541	0.71
180_V	264_G	0.540	0.71
11_N	15_D	0.540	0.71
20_L	133_V	0.538	0.70
244_P	264_G	0.538	0.70
4_L	60_Y	0.536	0.70
59_L	63_L	0.535	0.70
161_L	244_P	0.534	0.70
65_K	108_Y	0.533	0.70
191_L	245_D	0.533	0.70
122_G	126_A	0.533	0.70
7_L	51_F	0.533	0.70
19_L	73_V	0.532	0.69
29_K	33_W	0.531	0.69
74_L	79_P	0.531	0.69
46_A	65_K	0.530	0.69
90_L	147_L	0.530	0.69
13_L	175_L	0.528	0.69
135_R	138_K	0.528	0.69
161_L	277_Q	0.527	0.69
231_S	268_G	0.527	0.69
250_E	256_I	0.527	0.69
150_V	263_I	0.527	0.69
117_L	121_L	0.526	0.69
186_E	238_L	0.526	0.69
7_L	100_G	0.524	0.68
146_L	165_L	0.523	0.68
99_L	103_L	0.521	0.68
69_S	97_F	0.519	0.68
141_K	144_K	0.519	0.68
42_G	46_A	0.518	0.67
141_K	167_T	0.518	0.67
249_I	258_I	0.517	0.67
118_F	129_L	0.514	0.67
68_V	106_L	0.514	0.67
148_Y	250_E	0.512	0.67
31_K	34_R	0.511	0.66
4_L	52_L	0.510	0.66
134_F	138_K	0.509	0.66
241_G	266_S	0.509	0.66
208_L	280_L	0.508	0.66
206_D	217_D	0.508	0.66
126_A	130_I	0.506	0.66
99_L	127_Y	0.504	0.65
244_P	261_V	0.501	0.65
95_V	167_T	0.501	0.65
181_I	281_H	0.501	0.65
215_L	221_A	0.500	0.65

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
4xnjA	1	0.4683	14.3	0.956	Contact Map
2i1aA	2	0.3063	11.5	0.958	Contact Map
3wdoA	1	0.6937	10.8	0.958	Contact Map
3s8iA	2	0.331	9.4	0.959	Contact Map
3o7qA	1	0.4754	8.5	0.96	Contact Map
2hs1A	2	0.3134	8.1	0.96	Contact Map
4u4vA	1	0.4859	7.2	0.961	Contact Map
4ezcA	3	0.5282	5.9	0.963	Contact Map
2hahA	2	0.3521	5.5	0.963	Contact Map
2r9rB	3	0.4718	5.5	0.963	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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