Virul_fac_BrkB - PFAM28P - GREMLIN Contacts

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Virul_fac_BrkB - Virulence factor BrkB

PFAM:	PF03631	Sequences: QEDDGTLLAAALAYYTLLSLFPLLLLLVALLGLFGDDPALQDQLLDQLAGLLPGEAADLIQDLLESLASSASAGLLGLGLLLWSASGVFGALERALNRIWGVKERRSFLRRRLLSLGLTLLLGLLLLVSLALSVALPALLEWLARLLGLGLALVTLGLLRLLRWLVSLLLLTLLFALLYRFLPNRRVRWRDVLPGALVAAVLWELASLLFGLYLANFASYNSTYGSLGAVIVLLLWLYLSALILLLGAELNAVLERRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	258 (252)
Sequences:	64800 (45751)
Seq/√Len:	2882.0
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_D	249_E	3.387	1.00
4_D	98_R	3.251	1.00
7_L	11_A	2.686	1.00
176_A	189_W	2.656	1.00
6_T	242_L	2.611	1.00
90_G	112_R	2.588	1.00
176_A	196_A	2.524	1.00
96_L	248_A	2.519	1.00
195_G	251_N	2.440	1.00
160_R	163_R	2.372	1.00
10_A	15_Y	2.292	1.00
172_T	200_A	2.214	1.00
203_W	240_S	2.165	1.00
43_Q	46_D	2.111	1.00
4_D	94_R	2.098	1.00
66_S	69_S	2.084	1.00
55_E	58_D	2.060	1.00
206_A	239_L	2.036	1.00
97_N	184_N	2.031	1.00
188_R	191_D	1.998	1.00
61_Q	65_E	1.983	1.00
95_A	245_L	1.953	1.00
202_L	243_I	1.926	1.00
12_L	241_A	1.893	1.00
175_F	199_A	1.851	1.00
112_R	115_S	1.846	1.00
199_A	247_G	1.839	1.00
58_D	61_Q	1.827	1.00
172_T	197_L	1.792	1.00
212_L	216_N	1.773	1.00
8_L	98_R	1.763	1.00
180_R	189_W	1.742	1.00
58_D	62_D	1.719	1.00
116_L	120_L	1.703	1.00
204_E	207_S	1.703	1.00
74_G	77_G	1.657	1.00
210_F	214_L	1.655	1.00
93_E	115_S	1.655	1.00
191_D	254_L	1.652	1.00
7_L	94_R	1.639	1.00
107_S	110_R	1.634	1.00
47_Q	50_G	1.633	1.00
113_L	117_G	1.632	1.00
37_D	41_Q	1.616	1.00
110_R	114_L	1.598	1.00
172_T	193_L	1.579	1.00
74_G	81_L	1.578	1.00
4_D	8_L	1.574	1.00
194_P	197_L	1.573	1.00
54_G	58_D	1.570	1.00
57_A	61_Q	1.547	1.00
252_A	256_R	1.526	1.00
38_P	41_Q	1.520	1.00
198_V	250_L	1.511	1.00
179_Y	247_G	1.509	1.00
176_A	192_V	1.501	1.00
42_D	46_D	1.499	1.00
75_L	79_G	1.496	1.00
9_A	242_L	1.495	1.00
66_S	70_S	1.487	1.00
39_A	43_Q	1.485	1.00
177_L	181_F	1.476	1.00
59_L	62_D	1.474	1.00
3_D	101_G	1.470	1.00
62_D	65_E	1.462	1.00
179_Y	199_A	1.461	1.00
77_G	80_L	1.456	1.00
86_S	112_R	1.445	1.00
192_V	196_A	1.444	1.00
145_R	148_G	1.436	1.00
168_L	200_A	1.432	1.00
4_D	7_L	1.429	1.00
8_L	95_A	1.425	1.00
43_Q	47_Q	1.422	1.00
63_L	66_S	1.414	1.00
198_V	202_L	1.400	1.00
85_A	119_T	1.393	1.00
161_L	165_L	1.382	1.00
65_E	69_S	1.377	1.00
191_D	255_E	1.364	1.00
46_D	49_A	1.353	1.00
102_V	185_R	1.328	1.00
39_A	42_D	1.323	1.00
175_F	244_L	1.312	1.00
219_S	222_S	1.310	1.00
99_I	249_E	1.302	1.00
93_E	111_R	1.286	1.00
73_A	76_L	1.258	1.00
108_F	112_R	1.258	1.00
172_T	196_A	1.252	1.00
208_L	212_L	1.246	1.00
178_L	182_L	1.245	1.00
146_L	150_G	1.238	1.00
41_Q	45_L	1.232	1.00
67_L	70_S	1.205	1.00
176_A	193_L	1.196	1.00
250_L	254_L	1.185	1.00
38_P	42_D	1.178	1.00
187_V	192_V	1.178	1.00
65_E	68_A	1.174	1.00
45_L	61_Q	1.167	1.00
100_W	251_N	1.167	1.00
97_N	183_P	1.164	1.00
7_L	98_R	1.151	1.00
175_F	203_W	1.145	1.00
77_G	81_L	1.145	1.00
226_S	229_A	1.129	1.00
106_R	114_L	1.119	1.00
172_T	176_A	1.107	1.00
83_W	87_G	1.102	1.00
199_A	243_I	1.099	1.00
72_S	81_L	1.099	1.00
52_L	56_A	1.090	1.00
49_A	57_A	1.083	1.00
63_L	67_L	1.082	1.00
96_L	182_L	1.081	1.00
90_G	94_R	1.078	1.00
56_A	59_L	1.078	1.00
72_S	77_G	1.071	1.00
96_L	244_L	1.071	1.00
46_D	50_G	1.071	1.00
68_A	71_A	1.068	1.00
152_A	155_T	1.067	1.00
204_E	208_L	1.066	1.00
42_D	45_L	1.065	1.00
41_Q	44_L	1.062	1.00
93_E	182_L	1.060	1.00
12_L	245_L	1.060	1.00
109_L	113_L	1.052	1.00
14_Y	234_L	1.051	1.00
29_A	33_L	1.048	1.00
207_S	236_W	1.047	1.00
16_T	88_V	1.041	1.00
62_D	66_S	1.034	1.00
45_L	49_A	1.034	1.00
194_P	254_L	1.034	1.00
141_E	145_R	1.020	1.00
72_S	75_L	1.015	1.00
99_I	245_L	1.002	1.00
7_L	91_A	1.001	1.00
110_R	113_L	0.998	1.00
8_L	11_A	0.994	1.00
202_L	206_A	0.992	1.00
253_V	256_R	0.991	1.00
176_A	180_R	0.980	1.00
16_T	241_A	0.979	1.00
162_L	165_L	0.977	1.00
196_A	200_A	0.977	1.00
171_L	200_A	0.974	1.00
11_A	91_A	0.971	1.00
40_L	43_Q	0.966	1.00
242_L	246_L	0.966	1.00
76_L	79_G	0.965	1.00
37_D	40_L	0.959	1.00
5_G	245_L	0.958	1.00
16_T	237_L	0.958	1.00
75_L	78_L	0.955	1.00
59_L	63_L	0.955	1.00
155_T	160_R	0.953	1.00
194_P	198_V	0.948	1.00
237_L	241_A	0.941	1.00
87_G	112_R	0.937	1.00
146_L	149_L	0.935	1.00
142_W	146_L	0.933	1.00
206_A	243_I	0.932	1.00
90_G	115_S	0.925	1.00
102_V	184_N	0.923	1.00
163_R	167_S	0.918	1.00
74_G	78_L	0.916	1.00
12_L	95_A	0.914	1.00
238_Y	242_L	0.897	1.00
97_N	102_V	0.896	1.00
10_A	14_Y	0.896	1.00
147_L	150_G	0.890	1.00
135_A	138_A	0.885	1.00
54_G	57_A	0.884	1.00
151_L	154_V	0.883	1.00
73_A	79_G	0.876	1.00
104_E	111_R	0.874	1.00
195_G	199_A	0.870	1.00
60_I	63_L	0.864	1.00
5_G	242_L	0.853	1.00
161_L	164_W	0.852	1.00
5_G	246_L	0.850	1.00
166_V	169_L	0.842	1.00
111_R	114_L	0.842	1.00
133_S	137_P	0.836	1.00
213_Y	217_F	0.835	1.00
105_R	184_N	0.832	1.00
86_S	116_L	0.831	1.00
73_A	77_G	0.831	1.00
209_L	212_L	0.831	1.00
5_G	249_E	0.829	1.00
109_L	112_R	0.829	1.00
72_S	76_L	0.824	1.00
151_L	155_T	0.821	1.00
168_L	172_T	0.813	1.00
169_L	173_L	0.812	1.00
172_T	201_V	0.811	1.00
236_W	240_S	0.808	1.00
180_R	192_V	0.806	1.00
190_R	194_P	0.805	1.00
148_G	151_L	0.805	1.00
90_G	111_R	0.803	1.00
23_L	27_L	0.797	1.00
138_A	141_E	0.797	1.00
31_L	35_G	0.796	1.00
17_L	234_L	0.791	1.00
125_L	129_S	0.788	1.00
249_E	253_V	0.784	1.00
66_S	71_A	0.783	1.00
47_Q	51_L	0.781	1.00
142_W	145_R	0.781	1.00
7_L	10_A	0.779	1.00
173_L	176_A	0.774	1.00
214_L	217_F	0.773	1.00
12_L	92_L	0.769	1.00
41_Q	65_E	0.768	1.00
171_L	204_E	0.765	1.00
93_E	184_N	0.764	1.00
246_L	249_E	0.757	1.00
165_L	169_L	0.757	1.00
15_Y	19_S	0.753	1.00
55_E	59_L	0.752	1.00
200_A	204_E	0.748	1.00
175_F	200_A	0.747	1.00
15_Y	91_A	0.746	1.00
159_L	162_L	0.736	1.00
175_F	196_A	0.734	1.00
84_S	87_G	0.733	1.00
145_R	150_G	0.730	1.00
168_L	201_V	0.725	1.00
212_L	215_A	0.723	1.00
156_L	161_L	0.720	1.00
210_F	232_V	0.718	1.00
223_T	226_S	0.716	1.00
150_G	153_L	0.713	1.00
208_L	211_G	0.712	1.00
17_L	230_V	0.711	1.00
94_R	98_R	0.711	1.00
138_A	142_W	0.711	1.00
185_R	255_E	0.710	1.00
160_R	164_W	0.707	1.00
194_P	251_N	0.704	1.00
14_Y	18_L	0.698	1.00
137_P	141_E	0.696	1.00
67_L	71_A	0.694	1.00
6_T	9_A	0.692	1.00
18_L	235_L	0.690	1.00
224_Y	231_I	0.689	1.00
193_L	197_L	0.688	1.00
101_G	252_A	0.688	1.00
145_R	149_L	0.687	1.00
180_R	186_R	0.686	1.00
158_L	162_L	0.681	1.00
57_A	60_I	0.678	1.00
48_L	52_L	0.678	1.00
209_L	213_Y	0.676	1.00
201_V	205_L	0.675	1.00
140_L	159_L	0.673	1.00
128_V	131_A	0.672	1.00
86_S	115_S	0.671	1.00
108_F	111_R	0.667	1.00
148_G	152_A	0.666	1.00
168_L	204_E	0.666	1.00
49_A	54_G	0.663	1.00
52_L	57_A	0.662	1.00
10_A	238_Y	0.661	1.00
198_V	247_G	0.659	1.00
73_A	81_L	0.657	1.00
76_L	80_L	0.654	1.00
228_G	232_V	0.654	1.00
193_L	196_A	0.652	1.00
63_L	68_A	0.649	1.00
100_W	187_V	0.649	1.00
155_T	158_L	0.647	1.00
11_A	15_Y	0.642	1.00
26_L	30_L	0.641	1.00
45_L	48_L	0.639	1.00
187_V	191_D	0.632	1.00
191_D	195_G	0.631	1.00
141_E	144_A	0.631	1.00
169_L	172_T	0.631	1.00
5_G	8_L	0.631	1.00
233_L	237_L	0.627	1.00
129_S	132_L	0.623	1.00
197_L	201_V	0.623	1.00
35_G	38_P	0.620	1.00
13_A	241_A	0.618	1.00
99_I	252_A	0.617	1.00
205_L	209_L	0.612	1.00
189_W	193_L	0.610	1.00
18_L	231_I	0.607	1.00
220_Y	224_Y	0.604	1.00
215_A	218_A	0.603	1.00
78_L	81_L	0.602	1.00
96_L	99_I	0.602	1.00
78_L	82_L	0.599	1.00
139_L	142_W	0.596	1.00
29_A	74_G	0.594	1.00
158_L	161_L	0.592	1.00
118_L	182_L	0.592	1.00
90_G	93_E	0.592	1.00
130_L	134_V	0.592	1.00
48_L	51_L	0.591	1.00
214_L	232_V	0.590	1.00
235_L	239_L	0.590	1.00
241_A	245_L	0.588	1.00
102_V	187_V	0.585	1.00
15_Y	87_G	0.583	1.00
75_L	80_L	0.581	1.00
133_S	204_E	0.580	1.00
49_A	61_Q	0.580	1.00
190_R	193_L	0.577	1.00
45_L	57_A	0.574	1.00
201_V	204_E	0.570	1.00
89_F	118_L	0.570	1.00
133_S	207_S	0.569	1.00
123_G	127_L	0.568	1.00
221_N	226_S	0.566	1.00
79_G	83_W	0.566	1.00
76_L	81_L	0.565	1.00
72_S	79_G	0.563	1.00
224_Y	228_G	0.562	1.00
121_L	125_L	0.562	1.00
29_A	32_G	0.561	1.00
149_L	153_L	0.560	1.00
91_A	94_R	0.558	1.00
194_P	250_L	0.557	1.00
40_L	44_L	0.555	1.00
153_L	156_L	0.555	1.00
61_Q	64_L	0.553	1.00
89_F	93_E	0.553	1.00
179_Y	248_A	0.551	1.00
164_W	167_S	0.551	1.00
113_L	116_L	0.550	1.00
99_I	248_A	0.550	1.00
206_A	236_W	0.546	1.00
92_L	178_L	0.545	1.00
117_G	121_L	0.545	1.00
218_A	222_S	0.544	1.00
222_S	226_S	0.544	1.00
167_S	171_L	0.542	1.00
93_E	114_L	0.541	1.00
90_G	108_F	0.540	1.00
5_G	99_I	0.540	1.00
83_W	112_R	0.540	1.00
23_L	26_L	0.539	1.00
121_L	177_L	0.538	1.00
86_S	119_T	0.538	1.00
18_L	84_S	0.538	1.00
88_V	241_A	0.537	1.00
18_L	234_L	0.536	1.00
48_L	57_A	0.532	1.00
91_A	95_A	0.531	1.00
117_G	120_L	0.529	1.00
21_F	25_L	0.528	1.00
235_L	238_Y	0.528	1.00
231_I	234_L	0.526	1.00
229_A	232_V	0.525	1.00
147_L	151_L	0.524	1.00
205_L	208_L	0.522	1.00
159_L	163_R	0.522	1.00
42_D	61_Q	0.521	1.00
10_A	13_A	0.519	1.00
149_L	152_A	0.516	1.00
44_L	47_Q	0.516	1.00
104_E	184_N	0.515	1.00
131_A	134_V	0.515	1.00
134_V	137_P	0.513	1.00
179_Y	196_A	0.509	1.00
143_L	146_L	0.508	1.00
180_R	187_V	0.506	1.00
86_S	90_G	0.505	1.00
50_G	57_A	0.504	1.00
3_D	252_A	0.503	1.00
75_L	81_L	0.501	1.00
191_D	194_P	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
4nv5A	1	0.5349	14.7	0.937	Contact Map
3rlfF	1	0.4574	7.2	0.945	Contact Map
4humA	1	0.8295	5.3	0.948	Contact Map
3mktA	1	0.8372	5.1	0.949	Contact Map
3ne5A	3	0.6318	5.1	0.949	Contact Map
4q65A	1	0.2636	3.8	0.952	Contact Map
4p02A	1	0.4457	2.7	0.955	Contact Map
4mycA	2	0.3062	2.6	0.956	Contact Map
4httA	1	0.8256	2.5	0.956	Contact Map
4uvmA	1	0.2752	2.2	0.958	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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