TraN - PFAM28P - GREMLIN Contacts

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TraN - Type-1V conjugative transfer system mating pair stabilisation

PFAM:	PF06986	Sequences: CTLTSEVCTEGPETRTINGVPVTRDCWKYERTYQCSYPSANDCGALRNPGCTQVGSECLDDEGGVCVVYEQTYSCPEPTCTSTQLVCGGDVFCLDGDCEDISREANTDFGDAVSALAALAEAGKDFDPNNGLTIFKGKAMTCRKKVFGFSNCCKDKGWGLDLGLAKCSSEEKALAKAREKGLCHYVGTYCSKKVLGVCLTKKKSYCCFGSKLARIIQEQGRPQLGIGWGSAKSPDCRGFT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	240 (239)
Sequences:	691 (555)
Seq/√Len:	35.9
META:	0.724

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
183_C	207_C	6.502	1.00
190_C	198_C	5.640	1.00
93_C	98_C	5.032	1.00
208_F	221_R	4.303	1.00
10_E	28_K	3.747	1.00
184_H	228_W	3.715	1.00
8_C	26_C	3.500	1.00
214_R	218_E	3.017	1.00
149_F	159_G	2.951	1.00
226_I	237_R	2.839	1.00
227_G	235_D	2.766	1.00
171_E	174_L	2.707	1.00
109_F	113_V	2.652	1.00
14_T	21_P	2.634	1.00
141_T	204_S	2.593	1.00
14_T	23_T	2.575	1.00
185_Y	203_K	2.525	1.00
56_S	69_Y	2.523	1.00
16_T	21_P	2.522	1.00
155_D	178_R	2.483	1.00
178_R	205_Y	2.379	1.00
10_E	13_E	2.299	0.99
58_C	66_C	2.174	0.99
9_T	30_E	1.996	0.98
191_S	202_K	1.972	0.98
53_Q	71_Q	1.962	0.98
53_Q	56_S	1.951	0.98
111_D	115_A	1.923	0.98
184_H	218_E	1.922	0.98
194_V	197_V	1.893	0.98
51_C	75_C	1.868	0.97
143_R	200_T	1.837	0.97
149_F	158_W	1.821	0.97
121_E	125_D	1.809	0.97
6_E	31_R	1.800	0.97
217_Q	221_R	1.726	0.96
192_K	199_L	1.698	0.96
185_Y	205_Y	1.646	0.95
188_T	203_K	1.639	0.95
11_G	14_T	1.638	0.95
219_Q	222_P	1.630	0.94
220_G	223_Q	1.598	0.94
177_A	207_C	1.587	0.94
193_K	201_K	1.577	0.93
190_C	193_K	1.570	0.93
56_S	71_Q	1.549	0.93
57_E	70_E	1.542	0.93
221_R	228_W	1.534	0.92
41_N	44_G	1.529	0.92
1_C	35_C	1.508	0.92
133_T	136_K	1.503	0.92
229_G	234_P	1.488	0.91
169_S	172_K	1.485	0.91
191_S	200_T	1.476	0.91
9_T	28_K	1.430	0.89
177_A	183_C	1.412	0.89
177_A	182_L	1.411	0.89
47_R	50_G	1.395	0.88
192_K	200_T	1.387	0.88
139_A	204_S	1.383	0.88
100_D	103_R	1.374	0.87
217_Q	224_L	1.344	0.86
220_G	224_L	1.329	0.85
188_T	201_K	1.325	0.85
226_I	235_D	1.306	0.84
212_L	220_G	1.284	0.83
168_S	171_E	1.256	0.82
117_A	121_E	1.252	0.82
118_A	122_A	1.230	0.81
12_P	23_T	1.217	0.80
210_S	213_A	1.216	0.80
208_F	237_R	1.215	0.80
150_S	163_G	1.213	0.80
212_L	219_Q	1.206	0.79
93_C	96_G	1.204	0.79
19_G	22_V	1.180	0.78
3_L	6_E	1.178	0.78
87_C	93_C	1.171	0.77
159_G	165_A	1.168	0.77
159_G	164_L	1.140	0.75
91_V	94_L	1.137	0.75
87_C	98_C	1.135	0.75
158_W	163_G	1.127	0.75
194_V	199_L	1.126	0.74
159_G	163_G	1.125	0.74
193_K	198_C	1.119	0.74
184_H	214_R	1.094	0.72
176_K	180_K	1.075	0.71
113_V	213_A	1.072	0.71
176_K	179_E	1.065	0.70
140_M	207_C	1.048	0.69
158_W	165_A	1.043	0.69
175_A	179_E	1.040	0.68
111_D	119_L	1.037	0.68
56_S	72_T	1.023	0.67
121_E	128_P	1.009	0.66
189_Y	204_S	1.006	0.66
61_D	64_G	1.002	0.65
150_S	160_L	1.000	0.65
144_K	161_D	0.994	0.65
155_D	175_A	0.991	0.65
161_D	164_L	0.988	0.64
189_Y	232_K	0.986	0.64
229_G	236_C	0.981	0.64
42_D	57_E	0.981	0.64
220_G	239_F	0.978	0.64
178_R	203_K	0.976	0.63
20_V	45_A	0.974	0.63
208_F	217_Q	0.967	0.63
146_V	191_S	0.962	0.62
189_Y	198_C	0.960	0.62
113_V	116_L	0.957	0.62
189_Y	202_K	0.950	0.61
143_R	168_S	0.945	0.61
152_C	167_C	0.945	0.61
12_P	25_D	0.944	0.61
139_A	234_P	0.941	0.60
17_I	23_T	0.940	0.60
13_E	21_P	0.938	0.60
181_G	211_K	0.931	0.60
204_S	234_P	0.917	0.58
227_G	234_P	0.912	0.58
181_G	184_H	0.908	0.58
158_W	175_A	0.902	0.57
236_C	240_T	0.888	0.56
221_R	237_R	0.887	0.56
208_F	220_G	0.884	0.56
116_L	157_G	0.884	0.56
11_G	25_D	0.883	0.56
119_L	127_D	0.881	0.55
15_R	27_W	0.879	0.55
189_Y	193_K	0.878	0.55
54_V	74_S	0.877	0.55
236_C	239_F	0.876	0.55
17_I	21_P	0.874	0.55
135_F	167_C	0.872	0.55
211_K	219_Q	0.872	0.55
118_A	216_I	0.870	0.54
143_R	202_K	0.869	0.54
187_G	229_G	0.866	0.54
121_E	124_K	0.866	0.54
115_A	119_L	0.861	0.54
134_I	239_F	0.860	0.54
141_T	234_P	0.854	0.53
151_N	196_G	0.853	0.53
204_S	235_D	0.852	0.53
10_E	15_R	0.850	0.53
53_Q	73_Y	0.850	0.53
117_A	208_F	0.837	0.52
201_K	232_K	0.833	0.51
158_W	179_E	0.829	0.51
161_D	166_K	0.828	0.51
198_C	201_K	0.827	0.51
145_K	150_S	0.826	0.51
53_Q	69_Y	0.826	0.51
218_E	228_W	0.815	0.50
115_A	125_D	0.814	0.50
143_R	171_E	0.811	0.49
7_V	30_E	0.811	0.49
150_S	215_I	0.811	0.49
165_A	177_A	0.810	0.49
15_R	73_Y	0.806	0.49
157_G	160_L	0.805	0.49
94_L	97_D	0.798	0.48
87_C	95_D	0.791	0.48
157_G	163_G	0.790	0.48
141_T	227_G	0.789	0.47
142_C	153_C	0.789	0.47
207_C	228_W	0.785	0.47
214_R	239_F	0.784	0.47
50_G	71_Q	0.783	0.47
154_K	201_K	0.782	0.47
60_D	104_E	0.781	0.47
146_V	210_S	0.779	0.47
17_I	22_V	0.778	0.46
95_D	228_W	0.778	0.46
206_C	210_S	0.778	0.46
151_N	154_K	0.777	0.46
23_T	45_A	0.776	0.46
9_T	29_Y	0.775	0.46
162_L	165_A	0.774	0.46
190_C	199_L	0.773	0.46
14_T	17_I	0.772	0.46
177_A	228_W	0.768	0.46
26_C	29_Y	0.767	0.46
109_F	157_G	0.767	0.46
48_N	231_A	0.766	0.45
50_G	54_V	0.761	0.45
144_K	188_T	0.759	0.45
227_G	230_S	0.757	0.45
89_G	95_D	0.756	0.45
206_C	236_C	0.747	0.44
74_S	79_T	0.742	0.43
4_T	7_V	0.742	0.43
4_T	32_T	0.742	0.43
136_K	201_K	0.732	0.43
13_E	16_T	0.730	0.42
157_G	164_L	0.729	0.42
186_V	231_A	0.728	0.42
215_I	220_G	0.727	0.42
191_S	198_C	0.725	0.42
202_K	232_K	0.722	0.42
169_S	173_A	0.721	0.42
95_D	107_T	0.719	0.41
3_L	31_R	0.714	0.41
158_W	178_R	0.708	0.41
228_W	239_F	0.699	0.40
91_V	144_K	0.691	0.39
13_E	23_T	0.691	0.39
88_G	124_K	0.690	0.39
106_N	125_D	0.688	0.39
50_G	209_G	0.686	0.39
7_V	12_P	0.685	0.39
11_G	18_N	0.685	0.39
72_T	89_G	0.682	0.38
52_T	74_S	0.679	0.38
148_G	155_D	0.675	0.38
127_D	130_N	0.675	0.38
122_A	217_Q	0.674	0.38
86_V	232_K	0.673	0.38
120_A	124_K	0.672	0.38
6_E	29_Y	0.672	0.38
160_L	163_G	0.668	0.37
151_N	203_K	0.668	0.37
46_L	50_G	0.664	0.37
17_I	27_W	0.663	0.37
110_G	114_S	0.662	0.37
28_K	238_G	0.660	0.37
157_G	161_D	0.660	0.37
50_G	69_Y	0.655	0.36
217_Q	222_P	0.649	0.36
109_F	217_Q	0.648	0.36
63_G	67_V	0.648	0.36
4_T	9_T	0.646	0.35
26_C	87_C	0.645	0.35
189_Y	231_A	0.641	0.35
154_K	168_S	0.638	0.35
222_P	235_D	0.636	0.35
191_S	233_S	0.634	0.35
137_G	142_C	0.630	0.34
19_G	26_C	0.626	0.34
137_G	153_C	0.625	0.34
16_T	19_G	0.623	0.34
16_T	24_R	0.620	0.33
135_F	217_Q	0.620	0.33
228_W	238_G	0.617	0.33
214_R	228_W	0.617	0.33
107_T	195_L	0.612	0.33
87_C	96_G	0.612	0.33
140_M	170_E	0.608	0.32
53_Q	72_T	0.608	0.32
50_G	53_Q	0.607	0.32
190_C	202_K	0.606	0.32
157_G	179_E	0.605	0.32
141_T	188_T	0.604	0.32
149_F	165_A	0.602	0.32
39_S	42_D	0.601	0.32
112_A	230_S	0.598	0.32
190_C	196_G	0.596	0.32
230_S	234_P	0.595	0.32
155_D	158_W	0.594	0.31
143_R	150_S	0.593	0.31
99_E	112_A	0.592	0.31
49_P	59_L	0.592	0.31
193_K	199_L	0.591	0.31
237_R	240_T	0.590	0.31
73_Y	82_S	0.590	0.31
109_F	175_A	0.589	0.31
114_S	159_G	0.588	0.31
43_C	142_C	0.588	0.31
207_C	239_F	0.588	0.31
16_T	20_V	0.587	0.31
53_Q	74_S	0.586	0.31
80_C	183_C	0.584	0.31
151_N	205_Y	0.583	0.31
112_A	181_G	0.583	0.31
91_V	99_E	0.582	0.31
53_Q	59_L	0.579	0.30
61_D	67_V	0.577	0.30
145_K	151_N	0.575	0.30
18_N	29_Y	0.571	0.30
125_D	213_A	0.571	0.30
141_T	168_S	0.570	0.30
17_I	24_R	0.569	0.30
172_K	179_E	0.567	0.29
221_R	235_D	0.564	0.29
155_D	205_Y	0.563	0.29
24_R	27_W	0.563	0.29
12_P	21_P	0.562	0.29
109_F	120_A	0.562	0.29
158_W	161_D	0.561	0.29
175_A	207_C	0.560	0.29
54_V	174_L	0.560	0.29
212_L	215_I	0.559	0.29
164_L	175_A	0.558	0.29
144_K	180_K	0.556	0.29
26_C	51_C	0.554	0.29
26_C	75_C	0.554	0.29
6_E	9_T	0.553	0.28
146_V	208_F	0.552	0.28
11_G	15_R	0.550	0.28
86_V	184_H	0.550	0.28
25_D	28_K	0.545	0.28
56_S	70_E	0.543	0.28
193_K	204_S	0.542	0.28
47_R	64_G	0.541	0.28
181_G	195_L	0.540	0.28
17_I	39_S	0.539	0.27
7_V	22_V	0.538	0.27
16_T	23_T	0.537	0.27
38_P	52_T	0.535	0.27
50_G	56_S	0.534	0.27
36_S	240_T	0.534	0.27
49_P	53_Q	0.531	0.27
89_G	184_H	0.530	0.27
140_M	177_A	0.530	0.27
115_A	210_S	0.529	0.27
98_C	158_W	0.528	0.27
58_C	98_C	0.527	0.27
20_V	57_E	0.526	0.27
79_T	178_R	0.526	0.27
222_P	239_F	0.525	0.27
150_S	191_S	0.525	0.27
141_T	189_Y	0.525	0.27
154_K	179_E	0.524	0.26
18_N	104_E	0.524	0.26
2_T	25_D	0.523	0.26
41_N	94_L	0.523	0.26
154_K	212_L	0.522	0.26
15_R	19_G	0.522	0.26
70_E	188_T	0.521	0.26
211_K	214_R	0.520	0.26
83_T	188_T	0.519	0.26
10_E	23_T	0.518	0.26
39_S	240_T	0.518	0.26
135_F	152_C	0.518	0.26
7_V	19_G	0.517	0.26
123_G	203_K	0.517	0.26
156_K	179_E	0.515	0.26
192_K	202_K	0.513	0.26
184_H	239_F	0.511	0.26
166_K	205_Y	0.508	0.25
69_Y	74_S	0.508	0.25
75_C	206_C	0.508	0.25
61_D	70_E	0.508	0.25
13_E	25_D	0.507	0.25
195_L	211_K	0.506	0.25
102_S	107_T	0.506	0.25
12_P	79_T	0.506	0.25
22_V	27_W	0.506	0.25
12_P	29_Y	0.506	0.25
7_V	10_E	0.505	0.25
24_R	29_Y	0.505	0.25
119_L	203_K	0.503	0.25
5_S	32_T	0.503	0.25
77_E	177_A	0.502	0.25
16_T	22_V	0.500	0.25
12_P	53_Q	0.500	0.25

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
3t4rA	1	0.1125	3.2	0.973	Contact Map
3ssbC	1	0.1333	2.4	0.975	Contact Map
2mjkA	1	0.1542	2.3	0.975	Contact Map
2m0pA	1	0.1917	1.9	0.976	Contact Map
1ajjA	1	0.1542	1.8	0.977	Contact Map
1cr8A	1	0.1708	1.7	0.977	Contact Map
1eyoA	1	0.125	1.7	0.977	Contact Map
1k36A	1	0.1292	1.7	0.977	Contact Map
2jm4A	1	0.175	1.7	0.977	Contact Map
2m96A	1	0.1792	1.7	0.977	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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