T6SS_VasB - PFAM28P - GREMLIN Contacts

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T6SS_VasB - Type VI secretion, VasB, ImpH, VC_A0111

PFAM:	PF06996	Sequences: EPYRFDFFQAVRLLERPDRPRLGRAARPADEPVRFRQDPSLAFPPSEIASLERPEDDGPPRLTVNFLGLTGPNGPLPLHYTELALERRRAGDPALRDFLDIFNHRLLSLFYRAWAKYRPAVSYDRPGDDRFSRYLLALIGLGTPGLRGRAVPDEALLFYAGLLAQRPRSAEGLEAILSDYFGVPVEVEQFVGRWLPLPPDQRTRLGRANARLGVGAVLGSRVWDRQSKFRIRLGPLSLAQYERFLPGGDALRRLRALVRFYLGDELDWDVQLVLKAEEVPPLRLGGGGGPRLGWTTWLG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	299 (297)
Sequences:	5763 (4305)
Seq/√Len:	249.8
META:	0.738

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
192_G	223_W	3.800	1.00
159_Y	179_D	3.519	1.00
237_S	240_Q	3.184	1.00
172_G	261_Y	2.985	1.00
15_E	18_D	2.879	1.00
35_F	107_L	2.866	1.00
36_R	61_R	2.843	1.00
70_T	99_L	2.795	1.00
177_L	185_V	2.702	1.00
230_R	269_D	2.597	1.00
188_E	232_R	2.543	1.00
185_V	233_L	2.524	1.00
64_V	107_L	2.489	1.00
186_E	232_R	2.429	1.00
238_L	242_E	2.373	1.00
7_F	66_F	2.330	1.00
38_D	49_A	2.268	1.00
6_D	47_E	2.241	1.00
11_V	35_F	2.237	1.00
51_L	62_L	2.231	1.00
193_R	228_K	2.225	1.00
15_E	20_P	2.171	1.00
228_K	269_D	2.162	1.00
237_S	278_E	2.140	1.00
243_R	250_A	2.110	1.00
15_E	19_R	2.089	1.00
232_R	273_V	2.064	1.00
211_R	215_G	2.049	1.00
243_R	249_D	2.044	1.00
49_A	65_N	1.996	1.00
129_D	132_S	1.996	1.00
174_E	187_V	1.985	1.00
203_T	216_A	1.920	1.00
16_R	19_R	1.916	1.00
150_A	256_A	1.901	1.00
84_A	95_L	1.888	1.00
188_E	230_R	1.883	1.00
38_D	65_N	1.871	1.00
187_V	231_I	1.870	1.00
10_A	62_L	1.832	1.00
170_A	189_Q	1.826	1.00
240_Q	243_R	1.807	1.00
211_R	214_V	1.777	1.00
173_L	261_Y	1.755	1.00
230_R	271_Q	1.744	1.00
67_L	107_L	1.740	1.00
229_F	268_W	1.705	1.00
229_F	262_L	1.701	1.00
17_P	20_P	1.681	1.00
193_R	224_D	1.674	1.00
156_L	260_F	1.657	1.00
8_F	111_Y	1.657	1.00
181_F	254_L	1.649	1.00
36_R	63_T	1.646	1.00
104_H	108_S	1.642	1.00
242_E	291_R	1.627	1.00
149_R	153_D	1.618	1.00
174_E	178_S	1.604	1.00
236_L	272_L	1.596	1.00
231_I	258_V	1.595	1.00
232_R	271_Q	1.572	1.00
240_Q	250_A	1.567	1.00
237_S	275_K	1.557	1.00
181_F	244_F	1.557	1.00
100_D	103_N	1.552	1.00
174_E	186_E	1.547	1.00
194_W	221_R	1.544	1.00
87_R	92_D	1.521	1.00
198_P	201_Q	1.518	1.00
168_R	261_Y	1.515	1.00
25_A	31_E	1.511	1.00
183_V	233_L	1.486	1.00
196_P	221_R	1.477	1.00
96_R	100_D	1.472	1.00
10_A	48_I	1.465	1.00
177_L	231_I	1.455	1.00
136_L	157_L	1.444	1.00
191_V	230_R	1.408	1.00
70_T	103_N	1.403	1.00
93_P	97_D	1.380	1.00
275_K	278_E	1.369	1.00
136_L	147_R	1.338	1.00
95_L	99_L	1.330	1.00
9_Q	13_L	1.325	1.00
137_A	142_G	1.316	1.00
163_L	261_Y	1.312	1.00
123_Y	154_E	1.291	1.00
97_D	100_D	1.279	1.00
241_Y	274_L	1.276	1.00
233_L	236_L	1.263	1.00
199_P	202_R	1.245	1.00
282_L	290_P	1.241	1.00
229_F	258_V	1.238	1.00
194_W	223_W	1.230	1.00
39_P	70_T	1.230	1.00
114_W	121_V	1.221	1.00
86_E	89_R	1.217	1.00
7_F	11_V	1.213	1.00
184_P	234_G	1.208	1.00
70_T	84_A	1.204	1.00
141_L	260_F	1.203	1.00
67_L	106_L	1.203	1.00
188_E	191_V	1.196	1.00
176_I	261_Y	1.190	1.00
228_K	267_D	1.186	1.00
50_S	63_T	1.184	1.00
37_Q	103_N	1.182	1.00
191_V	228_K	1.182	1.00
12_R	124_D	1.178	1.00
8_F	114_W	1.173	1.00
16_R	20_P	1.165	1.00
229_F	266_L	1.163	1.00
158_F	179_D	1.152	1.00
180_Y	253_R	1.150	1.00
150_A	252_R	1.143	1.00
162_L	169_S	1.139	1.00
291_R	294_W	1.136	1.00
282_L	296_T	1.136	1.00
37_Q	70_T	1.133	1.00
139_I	160_A	1.129	1.00
195_L	224_D	1.128	1.00
151_V	257_L	1.126	1.00
162_L	175_A	1.125	1.00
171_E	174_E	1.124	1.00
52_E	61_R	1.124	1.00
85_L	88_R	1.121	1.00
36_R	100_D	1.119	1.00
197_L	217_V	1.104	1.00
51_L	60_P	1.099	1.00
84_A	96_R	1.098	1.00
224_D	227_S	1.096	1.00
248_G	252_R	1.091	1.00
259_R	264_D	1.080	1.00
54_P	61_R	1.080	1.00
111_Y	114_W	1.079	1.00
193_R	267_D	1.079	1.00
48_I	62_L	1.077	1.00
170_A	187_V	1.077	1.00
171_E	175_A	1.074	1.00
169_S	172_G	1.067	1.00
176_I	257_L	1.066	1.00
22_L	35_F	1.066	1.00
11_V	22_L	1.059	1.00
209_N	215_G	1.056	1.00
103_N	107_L	1.053	1.00
114_W	118_R	1.049	1.00
27_R	30_D	1.049	1.00
203_T	210_A	1.049	1.00
238_L	280_P	1.038	1.00
183_V	244_F	1.036	1.00
174_E	189_Q	1.033	1.00
273_V	276_A	1.027	1.00
204_R	208_A	1.024	1.00
34_R	59_P	1.022	1.00
242_E	295_T	1.020	1.00
130_R	133_R	1.018	1.00
163_L	260_F	1.012	1.00
234_G	273_V	1.008	1.00
250_A	253_R	1.000	1.00
180_Y	257_L	0.999	1.00
115_A	125_R	0.997	1.00
203_T	218_L	0.996	1.00
45_P	49_A	0.991	1.00
122_S	129_D	0.987	1.00
33_V	62_L	0.984	1.00
178_S	185_V	0.980	1.00
24_R	116_K	0.978	1.00
165_Q	169_S	0.976	1.00
22_L	108_S	0.971	1.00
258_V	268_W	0.970	1.00
274_L	278_E	0.968	1.00
247_G	291_R	0.966	1.00
291_R	295_T	0.956	1.00
208_A	211_R	0.951	1.00
49_A	63_T	0.946	1.00
123_Y	132_S	0.946	1.00
152_P	155_A	0.944	1.00
83_L	95_L	0.940	1.00
202_R	220_S	0.939	1.00
196_P	202_R	0.938	1.00
87_R	93_P	0.935	1.00
119_P	123_Y	0.933	1.00
9_Q	12_R	0.931	1.00
162_L	165_Q	0.924	1.00
192_G	225_R	0.921	1.00
132_S	157_L	0.919	1.00
86_E	90_A	0.917	1.00
151_V	154_E	0.914	1.00
146_L	149_R	0.913	1.00
285_G	290_P	0.912	1.00
38_D	63_T	0.904	1.00
22_L	32_P	0.904	1.00
103_N	106_L	0.902	1.00
233_L	244_F	0.902	1.00
236_L	240_Q	0.901	1.00
193_R	227_S	0.900	1.00
248_G	253_R	0.899	1.00
162_L	172_G	0.895	1.00
210_A	215_G	0.895	1.00
249_D	253_R	0.894	1.00
238_L	295_T	0.894	1.00
143_T	146_L	0.892	1.00
39_P	84_A	0.892	1.00
236_L	241_Y	0.890	1.00
141_L	156_L	0.889	1.00
67_L	110_F	0.879	1.00
88_R	93_P	0.877	1.00
23_G	112_R	0.877	1.00
239_A	242_E	0.877	1.00
173_L	258_V	0.875	1.00
139_I	156_L	0.868	0.99
139_I	157_L	0.866	0.99
28_P	31_E	0.865	0.99
203_T	209_N	0.861	0.99
20_P	30_D	0.860	0.99
123_Y	129_D	0.855	0.99
204_R	207_R	0.851	0.99
3_Y	46_S	0.851	0.99
196_P	220_S	0.849	0.99
252_R	255_R	0.843	0.99
254_L	270_V	0.840	0.99
246_P	294_W	0.840	0.99
41_L	81_T	0.833	0.99
233_L	270_V	0.829	0.99
119_P	131_F	0.827	0.99
5_F	10_A	0.823	0.99
31_E	108_S	0.822	0.99
3_Y	45_P	0.822	0.99
238_L	278_E	0.812	0.99
45_P	65_N	0.811	0.99
251_L	255_R	0.808	0.99
23_G	31_E	0.807	0.99
214_V	218_L	0.806	0.99
147_R	153_D	0.803	0.99
252_R	256_A	0.803	0.99
134_Y	137_A	0.798	0.99
69_L	103_N	0.798	0.99
37_Q	68_G	0.796	0.99
10_A	13_L	0.795	0.99
255_R	259_R	0.790	0.99
99_L	103_N	0.779	0.99
34_R	104_H	0.777	0.99
22_L	31_E	0.764	0.99
184_P	235_P	0.762	0.99
177_L	254_L	0.761	0.99
238_L	274_L	0.761	0.99
41_L	78_L	0.760	0.99
196_P	199_P	0.759	0.99
163_L	168_R	0.754	0.99
136_L	141_L	0.754	0.99
233_L	254_L	0.752	0.99
31_E	104_H	0.750	0.99
69_L	99_L	0.750	0.99
187_V	229_F	0.750	0.99
170_A	174_E	0.740	0.98
211_R	216_A	0.738	0.98
136_L	156_L	0.736	0.98
177_L	181_F	0.735	0.98
54_P	60_P	0.732	0.98
245_L	295_T	0.730	0.98
183_V	240_Q	0.728	0.98
131_F	134_Y	0.727	0.98
93_P	96_R	0.722	0.98
31_E	112_R	0.722	0.98
276_A	279_V	0.720	0.98
35_F	64_V	0.719	0.98
247_G	251_L	0.718	0.98
80_Y	99_L	0.717	0.98
47_E	66_F	0.715	0.98
21_R	24_R	0.709	0.98
282_L	298_L	0.708	0.98
12_R	125_R	0.706	0.98
82_E	86_E	0.703	0.98
244_F	250_A	0.697	0.98
64_V	67_L	0.695	0.98
245_L	272_L	0.695	0.98
195_L	227_S	0.693	0.98
55_E	58_G	0.691	0.97
290_P	296_T	0.689	0.97
177_L	180_Y	0.689	0.97
35_F	108_S	0.688	0.97
39_P	88_R	0.687	0.97
173_L	177_L	0.685	0.97
142_G	146_L	0.685	0.97
76_L	80_Y	0.684	0.97
130_R	134_Y	0.681	0.97
238_L	241_Y	0.677	0.97
186_E	234_G	0.677	0.97
53_R	60_P	0.676	0.97
7_F	64_V	0.672	0.97
87_R	96_R	0.669	0.97
205_L	210_A	0.669	0.97
191_V	269_D	0.668	0.97
135_L	160_A	0.668	0.97
247_G	294_W	0.667	0.97
54_P	59_P	0.666	0.97
39_P	81_T	0.664	0.97
247_G	253_R	0.664	0.97
178_S	184_P	0.663	0.97
181_F	233_L	0.660	0.97
162_L	171_E	0.660	0.97
5_F	13_L	0.657	0.97
23_G	28_P	0.657	0.97
10_A	14_L	0.655	0.97
2_P	5_F	0.653	0.96
156_L	257_L	0.652	0.96
48_I	66_F	0.650	0.96
155_A	180_Y	0.650	0.96
102_F	106_L	0.649	0.96
177_L	258_V	0.648	0.96
241_Y	297_W	0.646	0.96
181_F	250_A	0.643	0.96
122_S	125_R	0.641	0.96
207_R	210_A	0.640	0.96
148_G	153_D	0.637	0.96
118_R	121_V	0.636	0.96
151_V	155_A	0.635	0.96
181_F	185_V	0.634	0.96
174_E	185_V	0.633	0.96
159_Y	162_L	0.632	0.96
2_P	46_S	0.631	0.96
70_T	81_T	0.631	0.96
138_L	164_A	0.631	0.96
115_A	121_V	0.630	0.96
197_L	222_V	0.630	0.96
156_L	163_L	0.630	0.96
70_T	79_H	0.628	0.96
48_I	64_V	0.627	0.96
8_F	110_F	0.626	0.95
14_L	33_V	0.624	0.95
197_L	202_R	0.623	0.95
22_L	112_R	0.618	0.95
80_Y	84_A	0.617	0.95
70_T	78_L	0.616	0.95
32_P	108_S	0.616	0.95
22_L	25_A	0.616	0.95
198_P	253_R	0.616	0.95
174_E	231_I	0.615	0.95
245_L	294_W	0.613	0.95
40_S	65_N	0.609	0.95
290_P	295_T	0.607	0.95
256_A	260_F	0.606	0.95
23_G	108_S	0.606	0.95
246_P	251_L	0.604	0.95
44_P	49_A	0.600	0.94
188_E	271_Q	0.594	0.94
6_D	9_Q	0.594	0.94
23_G	29_A	0.592	0.94
54_P	57_D	0.591	0.94
149_R	256_A	0.591	0.94
206_G	210_A	0.591	0.94
279_V	297_W	0.590	0.94
41_L	82_E	0.589	0.94
70_T	100_D	0.589	0.94
104_H	112_R	0.586	0.94
283_R	286_G	0.585	0.94
63_T	97_D	0.585	0.94
28_P	32_P	0.585	0.94
240_Q	275_K	0.584	0.94
172_G	176_I	0.584	0.94
161_G	164_A	0.583	0.93
233_L	272_L	0.582	0.93
201_Q	209_N	0.579	0.93
119_P	132_S	0.577	0.93
22_L	28_P	0.573	0.93
77_P	80_Y	0.569	0.93
66_F	110_F	0.568	0.93
133_R	147_R	0.567	0.93
98_F	101_I	0.566	0.92
71_G	81_T	0.564	0.92
12_R	121_V	0.561	0.92
115_A	122_S	0.557	0.92
134_Y	138_L	0.557	0.92
212_L	216_A	0.556	0.92
256_A	261_Y	0.555	0.92
106_L	109_L	0.554	0.92
87_R	90_A	0.554	0.92
285_G	289_G	0.554	0.92
208_A	215_G	0.554	0.92
158_F	161_G	0.553	0.92
274_L	279_V	0.551	0.91
159_Y	176_I	0.550	0.91
205_L	298_L	0.549	0.91
37_Q	84_A	0.547	0.91
286_G	289_G	0.546	0.91
262_L	265_E	0.546	0.91
37_Q	107_L	0.545	0.91
40_S	81_T	0.544	0.91
251_L	270_V	0.544	0.91
24_R	231_I	0.543	0.91
44_P	72_P	0.543	0.91
188_E	269_D	0.543	0.91
39_P	85_L	0.543	0.91
43_F	46_S	0.542	0.91
115_A	119_P	0.542	0.91
14_L	60_P	0.541	0.91
143_T	147_R	0.540	0.91
39_P	96_R	0.539	0.91
234_G	278_E	0.539	0.91
108_S	112_R	0.539	0.91
85_L	91_G	0.538	0.90
50_S	58_G	0.534	0.90
92_D	98_F	0.533	0.90
244_F	292_L	0.533	0.90
239_A	278_E	0.533	0.90
78_L	81_T	0.531	0.90
237_S	241_Y	0.530	0.90
285_G	288_G	0.530	0.90
259_R	268_W	0.530	0.90
185_V	236_L	0.529	0.90
177_L	257_L	0.528	0.90
182_G	240_Q	0.526	0.89
25_A	28_P	0.526	0.89
36_R	96_R	0.525	0.89
200_D	208_A	0.524	0.89
86_E	92_D	0.522	0.89
173_L	187_V	0.522	0.89
204_R	220_S	0.522	0.89
119_P	122_S	0.522	0.89
249_D	252_R	0.522	0.89
37_Q	96_R	0.522	0.89
248_G	291_R	0.520	0.89
209_N	216_A	0.520	0.89
199_P	220_S	0.518	0.89
150_A	153_D	0.518	0.89
199_P	204_R	0.518	0.89
43_F	114_W	0.516	0.89
235_P	275_K	0.515	0.88
52_E	55_E	0.515	0.88
178_S	183_V	0.514	0.88
136_L	139_I	0.513	0.88
76_L	79_H	0.512	0.88
142_G	147_R	0.510	0.88
176_I	179_D	0.509	0.88
146_L	153_D	0.509	0.88
110_F	113_A	0.506	0.88
102_F	108_S	0.506	0.88
115_A	258_V	0.505	0.87
52_E	58_G	0.505	0.87
38_D	50_S	0.504	0.87
169_S	261_Y	0.504	0.87
274_L	297_W	0.503	0.87
68_G	72_P	0.503	0.87
132_S	154_E	0.501	0.87
88_R	96_R	0.500	0.87
91_G	263_G	0.500	0.87

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
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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
2d9rA	1	0.2542	8.4	0.967	Contact Map
4n6aA	3	0.7291	7.9	0.967	Contact Map
4mfgA	3	0.3478	7	0.968	Contact Map
3r3rA	3	0.3612	6.7	0.968	Contact Map
2eyxA	1	0.2074	6.4	0.968	Contact Map
3ixcA	3	0.3478	6.2	0.969	Contact Map
1ycsB	1	0.2676	5.9	0.969	Contact Map
4n78F	1	0	5.9	0.969	Contact Map
3r1wA	3	0.3545	5.4	0.97	Contact Map
4r36A	3	0.398	5.3	0.97	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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