Competence - PFAM28P - GREMLIN Contacts

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Competence - Competence protein

PFAM:	PF03772	Sequences: LLLGDRSGLDPELREAFRRTGLAHLLAISGLHVGIVAGLLFFLLRRLALRGPPRRLAALLALLALLLYALLTGASPSVVRAAIMAALVLLARLLGRRADPLNALALAALVLLLLDPLALFDVGFQLSFAAVAGILLLAPPLRRRLRRLPRLLRLAWALAVSLAAQLATLPLLLYYFGQVSLVGLLANLLAVPLVSLVVVPGALLALLLLLLPPLAALLAWLAGLLLALLLAVAEWLASLPGASLRVPAPPLWALLLYYLGLLLLLLLRRRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	271 (264)
Sequences:	40330 (32111)
Seq/√Len:	1976.3
META:	0.845

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_A	82_A	4.158	1.00
133_G	167_A	3.445	1.00
66_L	86_A	3.348	1.00
125_Q	175_Y	3.174	1.00
16_A	234_E	3.053	1.00
108_A	128_F	2.972	1.00
100_P	135_L	2.859	1.00
62_L	86_A	2.803	1.00
17_F	230_L	2.718	1.00
40_L	64_A	2.664	1.00
111_L	128_F	2.664	1.00
122_V	175_Y	2.394	1.00
227_A	231_A	2.344	1.00
66_L	82_A	2.325	1.00
186_A	236_L	2.155	1.00
130_A	168_T	2.133	1.00
15_E	19_R	2.118	1.00
231_A	235_W	2.064	1.00
134_I	160_V	2.063	1.00
14_R	18_R	2.018	1.00
70_L	74_A	1.984	1.00
137_L	163_A	1.973	1.00
231_A	234_E	1.967	1.00
189_L	192_P	1.957	1.00
111_L	118_A	1.934	1.00
133_G	164_A	1.902	1.00
69_A	74_A	1.849	1.00
112_L	118_A	1.846	1.00
28_I	78_V	1.842	1.00
37_A	85_A	1.828	1.00
101_L	136_L	1.821	1.00
69_A	78_V	1.808	1.00
65_L	82_A	1.800	1.00
223_G	227_A	1.796	1.00
115_D	118_A	1.787	1.00
220_W	224_L	1.775	1.00
18_R	23_A	1.770	1.00
217_L	221_L	1.741	1.00
44_L	60_L	1.741	1.00
83_I	107_A	1.734	1.00
108_A	124_F	1.704	1.00
16_A	233_A	1.678	1.00
193_L	228_L	1.648	1.00
101_L	132_A	1.639	1.00
178_Q	243_S	1.623	1.00
75_S	78_V	1.603	1.00
250_P	253_A	1.599	1.00
104_L	132_A	1.599	1.00
129_A	171_L	1.573	1.00
164_A	168_T	1.548	1.00
234_E	238_S	1.540	1.00
53_P	56_L	1.531	1.00
19_R	237_A	1.529	1.00
216_A	220_W	1.524	1.00
38_G	42_F	1.523	1.00
98_A	103_A	1.504	1.00
10_D	13_L	1.483	1.00
224_L	228_L	1.479	1.00
15_E	18_R	1.479	1.00
33_V	82_A	1.457	1.00
72_T	75_S	1.449	1.00
58_A	89_L	1.427	1.00
14_R	23_A	1.413	1.00
6_R	27_A	1.389	1.00
107_A	128_F	1.382	1.00
27_A	77_S	1.378	1.00
105_A	109_L	1.375	1.00
22_L	233_A	1.366	1.00
22_L	190_A	1.366	1.00
150_R	154_L	1.362	1.00
99_D	102_N	1.362	1.00
230_L	234_E	1.341	1.00
190_A	229_L	1.318	1.00
90_L	94_L	1.309	1.00
33_V	85_A	1.307	1.00
211_L	214_L	1.299	1.00
55_R	95_G	1.293	1.00
16_A	237_A	1.290	1.00
181_L	244_L	1.284	1.00
42_F	46_R	1.284	1.00
88_V	92_R	1.274	1.00
13_L	230_L	1.262	1.00
13_L	17_F	1.260	1.00
224_L	227_A	1.249	1.00
131_V	135_L	1.249	1.00
126_L	172_L	1.221	1.00
217_L	220_W	1.219	1.00
107_A	111_L	1.213	1.00
182_V	239_L	1.213	1.00
72_T	78_V	1.195	1.00
263_L	267_L	1.194	1.00
79_V	111_L	1.186	1.00
221_L	224_L	1.179	1.00
177_G	248_A	1.174	1.00
197_V	225_L	1.170	1.00
27_A	32_H	1.169	1.00
182_V	236_L	1.160	1.00
102_N	105_A	1.157	1.00
19_R	243_S	1.156	1.00
133_G	163_A	1.155	1.00
40_L	61_A	1.154	1.00
204_L	219_A	1.150	1.00
58_A	93_L	1.150	1.00
37_A	41_F	1.149	1.00
104_L	108_A	1.142	1.00
3_L	71_L	1.137	1.00
84_M	107_A	1.130	1.00
20_T	236_L	1.129	1.00
52_P	56_L	1.128	1.00
221_L	225_L	1.124	1.00
87_L	106_L	1.122	1.00
181_L	185_L	1.119	1.00
235_W	239_L	1.114	1.00
142_R	153_R	1.109	1.00
38_G	41_F	1.104	1.00
138_A	160_V	1.100	1.00
254_L	258_Y	1.099	1.00
22_L	186_A	1.097	1.00
17_F	26_L	1.095	1.00
200_P	204_L	1.095	1.00
182_V	242_A	1.075	1.00
19_R	178_Q	1.068	1.00
57_A	61_A	1.066	1.00
6_R	14_R	1.062	1.00
5_D	8_G	1.059	1.00
20_T	233_A	1.052	1.00
28_I	72_T	1.051	1.00
25_L	194_V	1.048	1.00
74_A	79_V	1.044	1.00
102_N	106_L	1.043	1.00
112_L	119_L	1.033	1.00
235_W	238_S	1.032	1.00
85_A	89_L	1.031	1.00
149_P	152_L	1.030	1.00
118_A	121_D	1.022	1.00
165_Q	168_T	1.018	1.00
220_W	223_G	1.018	1.00
132_A	136_L	1.018	1.00
13_L	16_A	1.014	1.00
58_A	62_L	1.012	1.00
122_V	176_F	1.011	1.00
189_L	232_V	1.006	1.00
16_A	230_L	1.003	1.00
41_F	61_A	0.999	1.00
125_Q	129_A	0.998	1.00
65_L	85_A	0.993	1.00
172_L	176_F	0.991	1.00
32_H	75_S	0.990	1.00
76_P	118_A	0.987	1.00
110_V	114_L	0.987	1.00
37_A	61_A	0.982	1.00
218_L	221_L	0.977	1.00
140_P	143_R	0.972	1.00
56_L	59_L	0.971	1.00
249_P	253_A	0.971	1.00
181_L	184_L	0.961	1.00
178_Q	181_L	0.957	1.00
194_V	229_L	0.956	1.00
138_A	142_R	0.955	1.00
82_A	86_A	0.953	1.00
140_P	144_R	0.953	1.00
149_P	153_R	0.946	1.00
25_L	190_A	0.946	1.00
51_G	56_L	0.944	1.00
111_L	124_F	0.938	1.00
31_L	34_G	0.933	1.00
154_L	158_L	0.930	1.00
103_A	107_A	0.926	1.00
153_R	157_A	0.911	1.00
213_P	217_L	0.907	1.00
204_L	222_A	0.904	1.00
249_P	258_Y	0.899	1.00
104_L	135_L	0.898	1.00
173_L	246_V	0.896	1.00
53_P	57_A	0.894	1.00
18_R	178_Q	0.892	1.00
171_L	175_Y	0.882	1.00
23_A	27_A	0.877	1.00
191_V	194_V	0.874	1.00
35_I	195_S	0.870	1.00
129_A	167_A	0.867	1.00
126_L	168_T	0.863	1.00
249_P	252_W	0.863	1.00
137_L	167_A	0.860	1.00
213_P	216_A	0.855	1.00
200_P	208_L	0.853	1.00
219_A	222_A	0.849	1.00
86_A	90_L	0.847	1.00
164_A	167_A	0.845	1.00
94_L	97_R	0.844	1.00
130_A	164_A	0.838	1.00
87_L	103_A	0.837	1.00
40_L	44_L	0.833	1.00
154_L	157_A	0.832	1.00
198_V	225_L	0.830	1.00
84_M	131_V	0.825	1.00
59_L	63_L	0.824	1.00
11_P	15_E	0.812	1.00
258_Y	261_L	0.811	1.00
37_A	89_L	0.807	1.00
228_L	231_A	0.806	1.00
36_V	64_A	0.804	1.00
160_V	164_A	0.799	1.00
125_Q	171_L	0.797	1.00
27_A	75_S	0.796	1.00
228_L	232_V	0.794	1.00
227_A	230_L	0.791	1.00
182_V	241_G	0.786	1.00
109_L	113_L	0.786	1.00
31_L	35_I	0.785	1.00
41_F	45_R	0.781	1.00
137_L	265_L	0.778	1.00
45_R	57_A	0.778	1.00
172_L	175_Y	0.775	1.00
37_A	65_L	0.772	1.00
1_L	194_V	0.769	1.00
59_L	93_L	0.767	1.00
199_V	202_A	0.766	1.00
252_W	255_L	0.764	1.00
232_V	236_L	0.764	1.00
210_L	213_P	0.760	1.00
44_L	57_A	0.759	1.00
165_Q	183_G	0.758	1.00
196_L	200_P	0.752	1.00
250_P	258_Y	0.751	1.00
187_N	191_V	0.750	1.00
200_P	222_A	0.745	1.00
152_L	156_W	0.743	1.00
151_L	154_L	0.743	1.00
66_L	69_A	0.742	1.00
28_I	33_V	0.741	1.00
168_T	172_L	0.736	1.00
2_L	202_A	0.733	1.00
171_L	258_Y	0.730	1.00
138_A	163_A	0.730	1.00
253_A	256_L	0.730	1.00
61_A	65_L	0.728	1.00
52_P	55_R	0.727	1.00
155_A	159_A	0.727	1.00
34_G	38_G	0.727	1.00
184_L	187_N	0.727	1.00
195_S	199_V	0.726	1.00
76_P	121_D	0.726	1.00
62_L	66_L	0.724	1.00
58_A	92_R	0.722	1.00
12_E	16_A	0.721	1.00
90_L	93_L	0.720	1.00
32_H	198_V	0.720	1.00
193_L	225_L	0.718	1.00
20_T	237_A	0.716	1.00
63_L	67_L	0.716	1.00
169_L	179_V	0.714	1.00
247_P	253_A	0.709	1.00
54_R	57_A	0.708	1.00
205_A	208_L	0.708	1.00
254_L	257_Y	0.705	1.00
77_S	123_G	0.703	1.00
215_A	219_A	0.703	1.00
174_Y	254_L	0.699	1.00
58_A	61_A	0.698	1.00
182_V	240_P	0.696	1.00
232_V	235_W	0.695	1.00
167_A	170_P	0.692	1.00
251_L	255_L	0.690	1.00
33_V	65_L	0.690	1.00
9_L	14_R	0.689	1.00
161_S	164_A	0.687	1.00
139_P	143_R	0.685	1.00
262_L	266_L	0.684	1.00
29_S	32_H	0.681	1.00
161_S	165_Q	0.680	1.00
31_L	191_V	0.679	1.00
129_A	175_Y	0.676	1.00
33_V	78_V	0.673	1.00
178_Q	245_R	0.672	1.00
206_L	209_L	0.668	1.00
42_F	45_R	0.667	1.00
83_I	111_L	0.664	1.00
236_L	239_L	0.664	1.00
47_L	51_G	0.664	1.00
169_L	172_L	0.662	1.00
88_V	98_A	0.659	1.00
202_A	208_L	0.659	1.00
41_F	57_A	0.659	1.00
255_L	258_Y	0.657	1.00
16_A	19_R	0.657	1.00
208_L	211_L	0.656	1.00
197_V	226_L	0.654	1.00
6_R	32_H	0.654	1.00
4_G	75_S	0.654	1.00
114_L	118_A	0.653	1.00
239_L	242_A	0.653	1.00
234_E	237_A	0.653	1.00
69_A	79_V	0.653	1.00
54_R	92_R	0.651	1.00
182_V	185_L	0.650	1.00
51_G	55_R	0.649	1.00
55_R	93_L	0.648	1.00
177_G	247_P	0.646	1.00
139_P	142_R	0.645	1.00
92_R	95_G	0.635	1.00
253_A	258_Y	0.631	1.00
255_L	259_L	0.630	1.00
28_I	32_H	0.630	1.00
222_A	225_L	0.628	1.00
62_L	89_L	0.628	1.00
134_I	163_A	0.622	1.00
195_S	200_P	0.621	1.00
229_L	233_A	0.620	1.00
226_L	230_L	0.619	1.00
67_L	70_L	0.619	1.00
249_P	257_Y	0.613	1.00
256_L	260_G	0.606	1.00
20_T	186_A	0.605	1.00
170_P	258_Y	0.604	1.00
198_V	202_A	0.600	1.00
66_L	70_L	0.600	1.00
174_Y	178_Q	0.599	1.00
245_R	248_A	0.598	1.00
188_L	192_P	0.597	1.00
156_W	159_A	0.593	1.00
161_S	187_N	0.593	1.00
184_L	188_L	0.593	1.00
106_L	110_V	0.590	1.00
31_L	195_S	0.589	1.00
219_A	223_G	0.588	1.00
91_A	98_A	0.588	1.00
87_L	110_V	0.587	1.00
206_L	210_L	0.586	1.00
33_V	69_A	0.585	1.00
214_L	217_L	0.583	1.00
21_G	183_G	0.583	1.00
212_P	216_A	0.580	1.00
163_A	167_A	0.580	1.00
144_R	148_L	0.580	1.00
208_L	212_P	0.579	1.00
205_A	209_L	0.578	1.00
247_P	250_P	0.578	1.00
67_L	71_L	0.577	1.00
98_A	102_N	0.576	1.00
257_Y	261_L	0.573	1.00
197_V	222_A	0.573	1.00
17_F	22_L	0.572	1.00
192_P	196_L	0.571	1.00
227_A	234_E	0.570	1.00
39_L	42_F	0.567	1.00
208_L	218_L	0.566	1.00
54_R	58_A	0.563	1.00
147_R	152_L	0.562	1.00
122_V	125_Q	0.561	1.00
197_V	229_L	0.560	1.00
160_V	191_V	0.559	1.00
195_S	198_V	0.558	1.00
149_P	155_A	0.557	1.00
151_L	156_W	0.557	1.00
207_L	211_L	0.555	1.00
13_L	26_L	0.555	1.00
79_V	83_I	0.553	1.00
56_L	60_L	0.549	1.00
251_L	254_L	0.546	1.00
99_D	103_A	0.544	1.00
100_P	103_A	0.543	1.00
151_L	155_A	0.542	1.00
142_R	146_R	0.541	1.00
44_L	52_P	0.539	1.00
150_R	153_R	0.538	1.00
260_G	263_L	0.537	1.00
142_R	157_A	0.537	1.00
174_Y	251_L	0.535	1.00
216_A	219_A	0.535	1.00
201_G	205_A	0.534	1.00
207_L	210_L	0.532	1.00
25_L	191_V	0.532	1.00
69_A	72_T	0.531	1.00
131_V	134_I	0.530	1.00
27_A	81_A	0.529	1.00
51_G	57_A	0.527	1.00
31_L	75_S	0.524	1.00
260_G	264_L	0.523	1.00
144_R	147_R	0.522	1.00
252_W	256_L	0.520	1.00
253_A	257_Y	0.518	1.00
194_V	198_V	0.517	1.00
191_V	195_S	0.513	1.00
205_A	219_A	0.513	1.00
258_Y	262_L	0.513	1.00
152_L	155_A	0.512	1.00
169_L	173_L	0.509	1.00
6_R	31_L	0.509	1.00
189_L	228_L	0.508	1.00
141_L	144_R	0.508	1.00
32_H	78_V	0.506	1.00
24_H	187_N	0.504	1.00
46_R	53_P	0.503	1.00
155_A	158_L	0.503	1.00
211_L	215_A	0.500	1.00

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
4c0kA	1	0.1771	3	0.956	Contact Map
3j7aW	1	0.0517	3	0.956	Contact Map
2uz0A	4	0.2177	2.9	0.956	Contact Map
2oyoA	4	0.2214	2.7	0.957	Contact Map
4rotA	4	0.2214	2.6	0.957	Contact Map
3c1lA	5	0.2214	2.6	0.957	Contact Map
4exqA	2	0.2066	2.5	0.958	Contact Map
2pfxA	3	0.2214	2.4	0.958	Contact Map
3qkgA	1	0.155	2.3	0.959	Contact Map
2oilA	1	0.2214	2	0.96	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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