TraC_F_IV - PFAM28P - GREMLIN Contacts

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TraC_F_IV - F pilus assembly Type-IV secretion system for plasmid transfer

PFAM:	PF11130	Sequences: PSFSDLLPYRAYDPESGLFLNDDGSVGFVFELTPLAGAGEETRDALEGLLSFDLPEGTPLQFILFASPDIDPYLDRYRAYRTELGRQGEHLRALARRRGLFLDKGVTGSLSAPWRGPLRDFRLFVSVKLPGKSKDPSESPLEELNDLRERLESTLKSAGLPPRRLDPEDLIRWLRRLFNPDPDAGGDAPPVDYDPGRPLREQLIDSDTRIDVEPDGLRFDGLPHRVVRVLSLKRFPE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	237 (231)
Sequences:	2350 (1830)
Seq/√Len:	120.4
META:	0.768

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_E	122_R	4.708	1.00
71_D	103_D	3.936	1.00
166_D	169_D	3.474	1.00
19_F	167_P	3.417	1.00
21_N	25_S	3.285	1.00
152_E	164_R	3.209	1.00
13_D	16_S	2.867	1.00
29_V	165_L	2.842	1.00
66_A	119_R	2.826	1.00
163_R	169_D	2.818	1.00
171_I	199_L	2.788	1.00
19_F	166_D	2.771	1.00
165_L	169_D	2.684	1.00
29_V	126_S	2.584	1.00
63_I	126_S	2.561	1.00
210_I	219_F	2.454	1.00
194_D	197_R	2.417	1.00
62_F	125_V	2.324	1.00
170_L	174_L	2.291	1.00
66_A	121_F	2.245	1.00
17_G	164_R	2.242	1.00
74_L	99_G	2.239	1.00
28_F	148_R	2.232	1.00
32_L	125_V	2.214	1.00
152_E	162_P	2.154	1.00
179_N	208_T	2.114	1.00
105_G	110_L	2.089	1.00
67_S	176_R	2.046	1.00
78_R	96_R	2.044	1.00
97_R	100_L	1.992	1.00
12_Y	19_F	1.983	1.00
9_Y	170_L	1.960	1.00
167_P	193_Y	1.954	1.00
92_R	96_R	1.946	1.00
232_L	235_F	1.938	1.00
32_L	123_L	1.910	1.00
30_F	162_P	1.890	1.00
17_G	166_D	1.868	1.00
30_F	152_E	1.839	1.00
9_Y	174_L	1.837	1.00
212_V	217_L	1.787	1.00
62_F	123_L	1.781	1.00
213_E	216_G	1.715	1.00
98_R	102_L	1.710	1.00
12_Y	17_G	1.685	1.00
104_K	108_G	1.652	1.00
25_S	128_K	1.637	1.00
21_N	24_G	1.626	1.00
171_I	193_Y	1.625	1.00
124_F	173_W	1.618	1.00
171_I	203_L	1.612	1.00
19_F	165_L	1.567	1.00
174_L	203_L	1.566	1.00
69_D	176_R	1.554	1.00
99_G	103_D	1.530	1.00
49_L	154_T	1.491	1.00
9_Y	21_N	1.479	1.00
148_R	164_R	1.465	1.00
32_L	162_P	1.455	1.00
31_E	124_F	1.415	1.00
67_S	120_D	1.413	1.00
219_F	227_V	1.409	1.00
100_L	104_K	1.387	1.00
17_G	148_R	1.347	1.00
124_F	165_L	1.338	1.00
77_Y	81_R	1.332	1.00
31_E	163_R	1.332	1.00
78_R	99_G	1.326	1.00
193_Y	199_L	1.325	1.00
70_I	74_L	1.310	1.00
213_E	218_R	1.309	1.00
10_R	200_R	1.303	1.00
28_F	127_V	1.300	1.00
210_I	217_L	1.299	1.00
28_F	164_R	1.297	1.00
180_P	225_R	1.267	1.00
16_S	141_L	1.265	1.00
30_F	164_R	1.254	0.99
218_R	226_V	1.246	0.99
93_A	96_R	1.213	0.99
171_I	202_Q	1.208	0.99
60_L	127_V	1.208	0.99
152_E	156_K	1.203	0.99
193_Y	202_Q	1.200	0.99
10_R	22_D	1.191	0.99
100_L	103_D	1.190	0.99
30_F	148_R	1.179	0.99
67_S	122_R	1.174	0.99
179_N	205_D	1.174	0.99
174_L	178_F	1.173	0.99
16_S	145_N	1.142	0.99
116_G	119_R	1.125	0.99
23_D	128_K	1.122	0.99
35_L	42_T	1.101	0.99
197_R	201_E	1.095	0.99
64_L	123_L	1.094	0.99
29_V	124_F	1.092	0.99
96_R	100_L	1.078	0.98
60_L	125_V	1.070	0.98
81_R	95_A	1.057	0.98
18_L	28_F	1.056	0.98
75_D	79_A	1.056	0.98
21_N	27_G	1.051	0.98
28_F	144_L	1.048	0.98
3_F	204_I	1.046	0.98
71_D	75_D	1.044	0.98
19_F	169_D	1.042	0.98
33_T	161_P	1.024	0.98
9_Y	203_L	0.998	0.97
19_F	170_L	0.997	0.97
38_A	42_T	0.991	0.97
35_L	38_A	0.980	0.97
54_L	58_T	0.980	0.97
211_D	218_R	0.966	0.97
69_D	172_R	0.956	0.97
93_A	97_R	0.949	0.96
76_R	79_A	0.946	0.96
9_Y	126_S	0.938	0.96
58_T	129_L	0.935	0.96
77_Y	90_H	0.934	0.96
26_V	131_G	0.928	0.96
7_L	179_N	0.925	0.96
187_D	190_P	0.919	0.96
173_W	177_L	0.918	0.96
14_P	17_G	0.910	0.95
22_D	200_R	0.907	0.95
165_L	173_W	0.904	0.95
27_G	119_R	0.904	0.95
165_L	170_L	0.890	0.95
153_S	157_S	0.885	0.95
45_A	157_S	0.885	0.95
132_K	137_S	0.884	0.95
20_L	26_V	0.877	0.94
41_E	45_A	0.876	0.94
72_P	76_R	0.874	0.94
141_L	145_N	0.872	0.94
77_Y	80_Y	0.853	0.94
31_E	120_D	0.844	0.93
40_E	44_D	0.841	0.93
188_A	192_D	0.841	0.93
167_P	171_I	0.840	0.93
209_R	221_G	0.835	0.93
75_D	78_R	0.826	0.93
32_L	160_L	0.822	0.92
38_A	43_R	0.819	0.92
182_P	220_D	0.818	0.92
41_E	44_D	0.817	0.92
220_D	224_H	0.817	0.92
49_L	121_F	0.805	0.92
155_L	160_L	0.805	0.92
30_F	165_L	0.802	0.91
74_L	103_D	0.797	0.91
89_E	94_L	0.786	0.91
215_D	218_R	0.783	0.90
153_S	184_A	0.783	0.90
227_V	234_R	0.782	0.90
71_D	106_V	0.778	0.90
32_L	155_L	0.778	0.90
202_Q	207_D	0.777	0.90
89_E	92_R	0.775	0.90
38_A	101_F	0.774	0.90
66_A	126_S	0.773	0.90
171_I	175_R	0.765	0.89
84_L	88_G	0.762	0.89
175_R	205_D	0.760	0.89
19_F	29_V	0.755	0.89
39_G	42_T	0.752	0.89
18_L	26_V	0.747	0.88
129_L	144_L	0.744	0.88
34_P	155_L	0.741	0.88
65_F	68_P	0.739	0.88
63_I	177_L	0.737	0.88
210_I	233_K	0.734	0.87
59_P	128_K	0.725	0.87
216_G	226_V	0.724	0.87
22_D	26_V	0.723	0.87
94_L	98_R	0.720	0.86
71_D	74_L	0.719	0.86
48_G	158_A	0.710	0.86
7_L	125_V	0.709	0.85
177_L	180_P	0.709	0.85
145_N	164_R	0.708	0.85
111_S	114_W	0.707	0.85
172_R	185_G	0.706	0.85
47_E	157_S	0.706	0.85
65_F	177_L	0.701	0.85
24_G	124_F	0.698	0.85
149_E	152_E	0.690	0.84
113_P	116_G	0.686	0.84
29_V	170_L	0.685	0.83
4_S	204_I	0.684	0.83
19_F	199_L	0.684	0.83
213_E	219_F	0.683	0.83
168_E	171_I	0.682	0.83
168_E	172_R	0.680	0.83
65_F	173_W	0.674	0.82
35_L	123_L	0.673	0.82
60_L	204_I	0.673	0.82
58_T	130_P	0.669	0.82
131_G	136_P	0.669	0.82
11_A	20_L	0.666	0.82
72_P	75_D	0.664	0.82
77_Y	98_R	0.664	0.82
167_P	199_L	0.662	0.81
69_D	160_L	0.660	0.81
170_L	193_Y	0.658	0.81
178_F	203_L	0.657	0.81
101_F	105_G	0.656	0.81
109_S	178_F	0.654	0.81
180_P	205_D	0.652	0.80
3_F	7_L	0.649	0.80
60_L	214_P	0.645	0.80
216_G	228_R	0.644	0.80
149_E	156_K	0.643	0.79
17_G	169_D	0.642	0.79
63_I	67_S	0.641	0.79
64_L	121_F	0.640	0.79
220_D	223_P	0.639	0.79
90_H	173_W	0.638	0.79
6_L	187_D	0.636	0.79
211_D	216_G	0.635	0.79
50_L	228_R	0.635	0.79
111_S	115_R	0.635	0.79
225_R	235_F	0.632	0.78
2_S	5_D	0.631	0.78
90_H	114_W	0.630	0.78
78_R	88_G	0.629	0.78
19_F	193_Y	0.626	0.78
228_R	234_R	0.626	0.78
19_F	164_R	0.624	0.77
25_S	144_L	0.620	0.77
32_L	35_L	0.619	0.77
204_I	208_T	0.615	0.76
103_D	106_V	0.613	0.76
30_F	39_G	0.609	0.76
117_P	178_F	0.608	0.76
54_L	59_P	0.607	0.75
151_L	192_D	0.606	0.75
50_L	106_V	0.606	0.75
85_G	143_E	0.606	0.75
55_P	170_L	0.605	0.75
79_A	86_R	0.605	0.75
145_N	148_R	0.605	0.75
39_G	56_E	0.604	0.75
13_D	155_L	0.602	0.75
62_F	121_F	0.602	0.75
49_L	151_L	0.601	0.75
59_P	126_S	0.600	0.75
183_D	186_G	0.597	0.74
131_G	140_P	0.596	0.74
89_E	141_L	0.593	0.74
179_N	203_L	0.592	0.74
65_F	122_R	0.591	0.73
184_A	233_K	0.590	0.73
21_N	128_K	0.590	0.73
25_S	38_A	0.589	0.73
20_L	166_D	0.588	0.73
25_S	46_L	0.586	0.73
86_R	89_E	0.586	0.73
53_D	150_R	0.585	0.73
65_F	176_R	0.584	0.73
146_D	156_K	0.584	0.73
78_R	95_A	0.583	0.72
69_D	181_D	0.578	0.72
33_T	40_E	0.578	0.72
13_D	26_V	0.577	0.72
119_R	122_R	0.576	0.72
102_L	207_D	0.574	0.71
209_R	214_P	0.574	0.71
47_E	124_F	0.572	0.71
73_Y	120_D	0.572	0.71
40_E	186_G	0.570	0.71
35_L	39_G	0.569	0.71
52_F	154_T	0.569	0.71
178_F	210_I	0.563	0.70
167_P	202_Q	0.563	0.70
136_P	140_P	0.562	0.70
88_G	92_R	0.562	0.70
132_K	136_P	0.562	0.70
48_G	167_P	0.561	0.70
46_L	206_S	0.560	0.69
123_L	176_R	0.560	0.69
214_P	218_R	0.556	0.69
46_L	73_Y	0.555	0.69
32_L	180_P	0.554	0.69
229_V	234_R	0.553	0.69
231_S	235_F	0.551	0.68
48_G	157_S	0.550	0.68
68_P	167_P	0.550	0.68
218_R	223_P	0.548	0.68
225_R	229_V	0.546	0.68
168_E	190_P	0.545	0.67
184_A	220_D	0.545	0.67
90_H	101_F	0.545	0.67
18_L	145_N	0.544	0.67
142_E	229_V	0.541	0.67
50_L	154_T	0.541	0.67
105_G	114_W	0.540	0.67
184_A	187_D	0.540	0.67
135_D	192_D	0.539	0.67
178_F	204_I	0.538	0.66
25_S	59_P	0.537	0.66
54_L	127_V	0.537	0.66
48_G	150_R	0.537	0.66
42_T	45_A	0.537	0.66
87_Q	91_L	0.536	0.66
153_S	156_K	0.535	0.66
17_G	168_E	0.535	0.66
7_L	203_L	0.535	0.66
46_L	134_K	0.534	0.66
157_S	230_L	0.534	0.66
5_D	61_Q	0.533	0.66
99_G	178_F	0.528	0.65
167_P	170_L	0.528	0.65
69_D	229_V	0.527	0.65
41_E	57_G	0.525	0.65
93_A	166_D	0.524	0.64
67_S	109_S	0.524	0.64
103_D	195_P	0.522	0.64
12_Y	214_P	0.519	0.64
41_E	209_R	0.519	0.64
3_F	183_D	0.518	0.64
180_P	220_D	0.518	0.64
41_E	153_S	0.517	0.63
26_V	205_D	0.517	0.63
96_R	113_P	0.515	0.63
46_L	197_R	0.515	0.63
34_P	39_G	0.514	0.63
218_R	221_G	0.511	0.62
45_A	121_F	0.510	0.62
156_K	210_I	0.510	0.62
132_K	145_N	0.509	0.62
105_G	118_L	0.507	0.62
180_P	184_A	0.507	0.62
86_R	108_G	0.507	0.62
122_R	169_D	0.507	0.62
135_D	153_S	0.507	0.62
16_S	148_R	0.507	0.62
29_V	174_L	0.506	0.62
5_D	201_E	0.506	0.62
50_L	125_V	0.505	0.62
85_G	88_G	0.504	0.61
104_K	188_A	0.504	0.61
198_P	201_E	0.504	0.61
45_A	158_A	0.500	0.61
86_R	163_R	0.500	0.61

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
3jygA	4	0.3165	10.2	0.946	Contact Map
3g1jA	1	0.2068	5	0.953	Contact Map
4p5eA	2	0.346	4.3	0.955	Contact Map
4ks9A	2	0.7384	3.8	0.956	Contact Map
3rnvA	3	0.2574	3.7	0.956	Contact Map
2e29A	1	0.2278	3.5	0.956	Contact Map
2m3dA	1	0.2363	2.7	0.959	Contact Map
4m2aA	1	0.3544	2.7	0.959	Contact Map
1wf3A	1	0.5949	2.6	0.959	Contact Map
2ejsA	1	0.2447	2.6	0.959	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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