CagE_TrbE_VirB - PFAM28P - GREMLIN Contacts

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CagE_TrbE_VirB - CagE, TrbE, VirB family, component of type IV transporter system

PFAM:	PF03135	Sequences: RLLGVYEGNGLLFSELLEFLHSLINGERHPVPLPEGMYLDALLATGRLPFGGDALEIRGAPGTRFPGILSIKEYPFETRWGTRDILLDLPFEFVLTQSFRFLWRQKARGLLDRQQRRMASADDDAVSQAADLDAALDELGSGRVAFGYHHLTVVVFDEDLEELDEKVAEVRKALQDLGFVAVREDLNAEEAFLGQLPGNFYANVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	205 (197)
Sequences:	4546 (2807)
Seq/√Len:	200.0
META:	0.791

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_D	162_E	4.200	1.00
157_D	166_K	3.327	1.00
55_L	66_P	2.973	1.00
127_S	137_D	2.971	1.00
159_D	162_E	2.811	1.00
153_V	170_V	2.332	1.00
68_I	154_V	2.289	1.00
138_E	143_R	2.257	1.00
56_E	61_P	2.247	1.00
46_G	51_G	2.197	1.00
157_D	163_L	2.153	1.00
46_G	49_P	2.126	1.00
67_G	167_V	2.112	1.00
56_E	60_A	2.101	1.00
51_G	54_A	2.045	1.00
155_V	163_L	2.039	1.00
21_H	25_N	2.035	1.00
57_I	60_A	2.018	1.00
57_I	61_P	1.967	1.00
49_P	54_A	1.856	1.00
139_L	146_F	1.822	1.00
18_E	30_P	1.818	1.00
56_E	59_G	1.812	1.00
14_S	33_L	1.791	1.00
199_N	202_A	1.776	1.00
104_R	107_A	1.754	1.00
55_L	60_A	1.719	1.00
106_K	109_G	1.714	1.00
163_L	167_V	1.710	1.00
154_V	195_Q	1.696	1.00
99_F	147_G	1.676	1.00
189_E	193_L	1.675	1.00
162_E	166_K	1.661	1.00
49_P	53_D	1.638	1.00
25_N	44_A	1.615	1.00
46_G	50_F	1.612	1.00
50_F	53_D	1.586	1.00
50_F	54_A	1.582	1.00
84_D	147_G	1.533	1.00
21_H	31_V	1.526	1.00
95_L	153_V	1.524	1.00
55_L	59_G	1.510	1.00
13_F	18_E	1.506	1.00
173_A	176_D	1.477	1.00
91_F	166_K	1.471	1.00
49_P	52_G	1.470	1.00
47_R	50_F	1.455	1.00
152_T	194_G	1.444	1.00
22_S	28_R	1.443	1.00
104_R	142_G	1.438	1.00
55_L	61_P	1.437	1.00
64_R	156_F	1.410	1.00
81_G	84_D	1.404	1.00
18_E	28_R	1.401	1.00
13_F	32_P	1.398	1.00
160_L	164_D	1.396	1.00
59_G	62_G	1.396	1.00
21_H	29_H	1.391	1.00
17_L	31_V	1.382	1.00
24_I	43_L	1.361	1.00
152_T	191_A	1.353	1.00
39_L	43_L	1.340	1.00
165_E	169_E	1.338	1.00
69_L	181_A	1.333	1.00
152_T	195_Q	1.332	1.00
115_Q	133_D	1.331	1.00
135_A	146_F	1.327	1.00
98_S	150_H	1.316	1.00
58_R	62_G	1.312	1.00
47_R	51_G	1.309	1.00
17_L	39_L	1.296	1.00
174_L	181_A	1.277	1.00
48_L	51_G	1.276	1.00
36_G	42_L	1.260	1.00
96_T	150_H	1.255	1.00
171_R	181_A	1.246	1.00
126_V	130_A	1.237	1.00
64_R	158_E	1.229	1.00
114_Q	118_M	1.228	1.00
116_R	120_S	1.226	1.00
21_H	44_A	1.191	1.00
103_W	106_K	1.178	1.00
19_F	23_L	1.176	1.00
115_Q	119_A	1.174	1.00
196_L	199_N	1.173	1.00
167_V	183_R	1.153	1.00
93_F	97_Q	1.151	1.00
161_E	165_E	1.129	1.00
48_L	52_G	1.125	1.00
21_H	45_T	1.106	1.00
155_V	170_V	1.094	1.00
184_E	187_N	1.093	1.00
16_L	19_F	1.076	1.00
70_S	73_E	1.064	1.00
58_R	61_P	1.053	1.00
48_L	54_A	1.041	1.00
114_Q	117_R	1.041	1.00
133_D	136_L	1.037	1.00
187_N	191_A	1.026	1.00
15_E	18_E	1.025	1.00
96_T	195_Q	1.025	1.00
11_L	32_P	1.025	1.00
124_D	136_L	1.007	1.00
55_L	154_V	1.007	1.00
70_S	74_Y	1.004	1.00
25_N	46_G	1.002	1.00
194_G	204_V	0.992	1.00
112_D	136_L	0.988	1.00
171_R	175_Q	0.986	1.00
72_K	180_V	0.983	1.00
116_R	119_A	0.982	1.00
57_I	62_G	0.974	0.99
160_L	163_L	0.970	0.99
47_R	185_D	0.968	0.99
107_A	113_R	0.968	0.99
109_G	113_R	0.965	0.99
66_P	154_V	0.959	0.99
104_R	113_R	0.958	0.99
187_N	204_V	0.947	0.99
123_D	127_S	0.947	0.99
80_W	83_R	0.937	0.99
66_P	156_F	0.937	0.99
26_G	156_F	0.933	0.99
194_G	203_N	0.925	0.99
19_F	22_S	0.924	0.99
105_Q	108_R	0.913	0.99
129_A	133_D	0.912	0.99
47_R	54_A	0.908	0.99
46_G	54_A	0.903	0.99
90_P	93_F	0.903	0.99
108_R	136_L	0.896	0.99
24_I	196_L	0.885	0.99
14_S	17_L	0.884	0.99
71_I	179_F	0.884	0.99
39_L	44_A	0.879	0.99
158_E	162_E	0.873	0.99
39_L	42_L	0.869	0.99
13_F	16_L	0.863	0.99
95_L	98_S	0.859	0.99
131_D	141_S	0.839	0.98
187_N	203_N	0.838	0.98
122_D	140_G	0.836	0.98
97_Q	100_R	0.825	0.98
40_D	44_A	0.825	0.98
64_R	92_E	0.825	0.98
27_E	175_Q	0.822	0.98
159_D	163_L	0.820	0.98
105_Q	109_G	0.815	0.98
113_R	117_R	0.815	0.98
25_N	45_T	0.810	0.98
137_D	141_S	0.809	0.98
16_L	20_L	0.802	0.98
134_A	138_E	0.801	0.98
69_L	167_V	0.799	0.98
136_L	140_G	0.798	0.98
48_L	53_D	0.792	0.98
46_G	52_G	0.792	0.98
54_A	160_L	0.790	0.98
56_E	63_T	0.788	0.98
153_V	174_L	0.786	0.98
162_E	165_E	0.783	0.98
164_D	168_A	0.783	0.98
123_D	128_Q	0.780	0.98
12_L	16_L	0.778	0.98
117_R	120_S	0.772	0.97
95_L	99_F	0.763	0.97
97_Q	149_H	0.753	0.97
175_Q	181_A	0.749	0.97
112_D	124_D	0.746	0.97
46_G	53_D	0.737	0.97
31_V	180_V	0.736	0.97
9_N	13_F	0.736	0.97
155_V	166_K	0.733	0.96
108_R	140_G	0.732	0.96
89_L	173_A	0.727	0.96
76_F	166_K	0.727	0.96
70_S	184_E	0.725	0.96
119_A	129_A	0.725	0.96
163_L	166_K	0.723	0.96
129_A	132_L	0.723	0.96
115_Q	136_L	0.723	0.96
115_Q	120_S	0.722	0.96
93_F	153_V	0.721	0.96
13_F	30_P	0.719	0.96
104_R	108_R	0.714	0.96
67_G	183_R	0.712	0.96
34_P	42_L	0.712	0.96
123_D	132_L	0.707	0.96
126_V	129_A	0.703	0.96
74_Y	149_H	0.701	0.95
190_E	193_L	0.700	0.95
62_G	158_E	0.692	0.95
65_F	86_L	0.688	0.95
97_Q	101_F	0.688	0.95
97_Q	151_L	0.682	0.95
156_F	166_K	0.682	0.95
94_V	156_F	0.681	0.95
47_R	52_G	0.676	0.94
12_L	15_E	0.674	0.94
69_L	171_R	0.672	0.94
200_F	203_N	0.669	0.94
95_L	151_L	0.668	0.94
193_L	199_N	0.666	0.94
55_L	58_R	0.663	0.94
184_E	191_A	0.662	0.94
108_R	112_D	0.655	0.94
192_F	202_A	0.652	0.93
91_F	170_V	0.649	0.93
71_I	74_Y	0.648	0.93
18_E	31_V	0.648	0.93
10_G	13_F	0.647	0.93
78_T	82_T	0.641	0.93
78_T	83_R	0.641	0.93
169_E	173_A	0.628	0.92
169_E	172_K	0.628	0.92
174_L	185_D	0.627	0.92
118_M	121_A	0.625	0.92
161_E	164_D	0.622	0.92
115_Q	118_M	0.621	0.92
121_A	125_A	0.618	0.91
66_P	92_E	0.613	0.91
131_D	135_A	0.612	0.91
92_E	166_K	0.607	0.91
138_E	146_F	0.606	0.91
112_D	138_E	0.601	0.90
190_E	194_G	0.600	0.90
72_K	182_V	0.598	0.90
132_L	136_L	0.598	0.90
171_R	183_R	0.595	0.90
85_I	173_A	0.594	0.90
105_Q	112_D	0.592	0.90
56_E	62_G	0.587	0.89
64_R	159_D	0.585	0.89
127_S	143_R	0.583	0.89
124_D	128_Q	0.582	0.89
17_L	34_P	0.579	0.89
125_A	141_S	0.579	0.89
115_Q	129_A	0.579	0.89
99_F	123_D	0.578	0.88
106_K	110_L	0.577	0.88
106_K	122_D	0.576	0.88
123_D	130_A	0.576	0.88
156_F	192_F	0.575	0.88
107_A	129_A	0.572	0.88
103_W	124_D	0.572	0.88
164_D	185_D	0.570	0.88
82_T	151_L	0.568	0.88
37_M	99_F	0.568	0.88
124_D	127_S	0.568	0.88
50_F	55_L	0.567	0.88
55_L	68_I	0.566	0.87
24_I	44_A	0.566	0.87
27_E	171_R	0.565	0.87
47_R	168_A	0.562	0.87
114_Q	120_S	0.562	0.87
139_L	145_A	0.562	0.87
71_I	173_A	0.562	0.87
118_M	129_A	0.560	0.87
97_Q	136_L	0.560	0.87
111_L	144_V	0.550	0.86
85_I	116_R	0.550	0.86
138_E	141_S	0.548	0.86
150_H	195_Q	0.545	0.85
54_A	158_E	0.543	0.85
31_V	35_E	0.539	0.85
95_L	192_F	0.539	0.85
71_I	177_L	0.539	0.85
150_H	203_N	0.537	0.85
68_I	191_A	0.536	0.84
88_D	103_W	0.536	0.84
48_L	57_I	0.535	0.84
51_G	56_E	0.534	0.84
23_L	94_V	0.531	0.84
131_D	138_E	0.530	0.84
75_P	145_A	0.529	0.84
175_Q	180_V	0.527	0.83
46_G	57_I	0.523	0.83
188_A	193_L	0.523	0.83
124_D	140_G	0.521	0.83
33_L	36_G	0.521	0.83
14_S	32_P	0.521	0.83
79_R	159_D	0.521	0.83
87_L	148_Y	0.521	0.83
99_F	145_A	0.518	0.82
125_A	128_Q	0.517	0.82
193_L	202_A	0.517	0.82
102_L	144_V	0.517	0.82
38_Y	43_L	0.515	0.82
105_Q	113_R	0.508	0.81
74_Y	98_S	0.506	0.81
102_L	107_A	0.505	0.81
114_Q	136_L	0.503	0.81
68_I	184_E	0.502	0.80
24_I	39_L	0.501	0.80
71_I	134_A	0.500	0.80
18_E	29_H	0.500	0.80

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
4dndA	1	0.4634	11.8	0.939	Contact Map
4j2cA	1	0.5317	11.3	0.94	Contact Map
2jvfA	1	0.4537	9.2	0.942	Contact Map
3ig3A	1	0.3415	7.5	0.944	Contact Map
1vp2A	3	0.4146	4.9	0.949	Contact Map
2z30B	1	0.2341	4.6	0.95	Contact Map
1vqzA	1	0.4195	4.5	0.95	Contact Map
1cg2A	4	0.3902	3.9	0.951	Contact Map
4c3sA	2	0.3805	3.8	0.951	Contact Map
4macA	2	0.3317	3.7	0.952	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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