TrbL - PFAM28P - GREMLIN Contacts

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TrbL - TrbL/VirB6 plasmid conjugal transfer protein

PFAM:	PF04610	Sequences: LTIYIALAGLRLALGRIGEPLAELVKKILKIGFFLALATNWPAYATIIVDSFTGLGLEAAGAILGAADLLASPALDQLGFDAADPLLDQASSLSFFGNIGAILALLLAWLIVLLAFAIAAAQLLLAKIALALLLALGPIFIPFLLFPKTRFLFEGWLGAVLSYGLKLVVLALIVGIGLTLLDSFLAALAAGAAPTLADALALLLAALVLLLLLIQV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	216 (213)
Sequences:	7718 (5625)
Seq/√Len:	385.4
META:	0.795

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_P	150_R	4.463	1.00
155_G	158_G	4.268	1.00
144_L	153_F	3.853	1.00
133_L	159_A	3.563	1.00
151_F	154_E	2.978	1.00
137_G	156_W	2.621	1.00
33_F	37_L	2.616	1.00
81_D	84_D	2.559	1.00
129_A	163_Y	2.541	1.00
50_D	54_G	2.431	1.00
46_T	50_D	2.378	1.00
7_L	11_R	2.375	1.00
150_R	154_E	2.254	1.00
140_F	152_L	2.197	1.00
26_K	30_K	2.190	1.00
81_D	85_P	2.106	1.00
129_A	166_K	2.001	1.00
151_F	155_G	2.000	1.00
136_L	169_V	1.995	1.00
154_E	158_G	1.993	1.00
133_L	160_V	1.960	1.00
75_L	78_L	1.869	1.00
35_L	39_T	1.827	1.00
79_G	83_A	1.808	1.00
143_F	152_L	1.806	1.00
119_A	213_L	1.800	1.00
4_Y	27_K	1.759	1.00
44_Y	137_G	1.733	1.00
159_A	163_Y	1.666	1.00
151_F	158_G	1.657	1.00
159_A	162_S	1.642	1.00
36_A	44_Y	1.613	1.00
6_A	10_L	1.611	1.00
34_F	144_L	1.580	1.00
177_G	209_L	1.566	1.00
10_L	14_L	1.557	1.00
89_Q	92_S	1.544	1.00
5_I	9_G	1.532	1.00
108_A	115_A	1.521	1.00
136_L	172_L	1.507	1.00
205_A	209_L	1.502	1.00
130_L	160_V	1.498	1.00
24_L	28_I	1.493	1.00
142_P	145_L	1.490	1.00
41_W	44_Y	1.489	1.00
17_I	20_P	1.470	1.00
136_L	168_V	1.465	1.00
41_W	45_A	1.462	1.00
43_A	47_I	1.429	1.00
80_F	84_D	1.425	1.00
178_L	182_D	1.398	1.00
48_I	51_S	1.377	1.00
152_L	158_G	1.368	1.00
140_F	153_F	1.364	1.00
11_R	16_R	1.350	1.00
126_A	166_K	1.346	1.00
57_L	61_G	1.340	1.00
197_A	200_L	1.333	1.00
167_L	171_A	1.313	1.00
85_P	88_D	1.306	1.00
74_A	78_L	1.297	1.00
68_D	71_A	1.288	1.00
123_L	127_K	1.287	1.00
140_F	143_F	1.284	1.00
146_F	149_T	1.268	1.00
135_A	138_P	1.264	1.00
9_G	13_A	1.246	1.00
166_K	170_L	1.244	1.00
162_S	166_K	1.236	1.00
153_F	157_L	1.234	1.00
84_D	88_D	1.219	1.00
51_S	54_G	1.215	1.00
200_L	208_V	1.214	1.00
54_G	57_L	1.213	1.00
2_T	6_A	1.200	1.00
36_A	40_N	1.199	1.00
204_L	209_L	1.189	1.00
138_P	156_W	1.176	1.00
75_L	79_G	1.174	1.00
202_L	206_A	1.170	1.00
54_G	58_E	1.167	1.00
140_F	165_L	1.159	1.00
57_L	60_A	1.159	1.00
201_A	209_L	1.152	1.00
85_P	89_Q	1.148	1.00
52_F	160_V	1.127	1.00
90_A	93_L	1.127	1.00
80_F	83_A	1.122	1.00
102_I	106_L	1.107	1.00
22_A	26_K	1.100	1.00
199_A	202_L	1.097	1.00
22_A	25_V	1.078	1.00
49_V	53_T	1.071	1.00
127_K	131_A	1.070	1.00
197_A	201_A	1.068	1.00
50_D	53_T	1.068	1.00
210_L	214_I	1.067	1.00
111_I	203_L	1.066	1.00
51_S	55_L	1.061	1.00
157_L	161_L	1.060	1.00
140_F	156_W	1.059	1.00
7_L	14_L	1.056	1.00
8_A	24_L	1.047	1.00
171_A	175_G	1.043	1.00
29_L	32_G	1.043	1.00
52_F	164_G	1.032	1.00
202_L	209_L	1.029	1.00
55_L	58_E	1.028	1.00
15_G	18_G	1.023	1.00
130_L	134_L	1.022	1.00
129_A	133_L	1.016	1.00
88_D	92_S	1.009	1.00
153_F	156_W	0.991	1.00
53_T	56_G	0.982	1.00
196_L	200_L	0.981	1.00
163_Y	167_L	0.976	1.00
141_I	153_F	0.963	1.00
201_A	205_A	0.958	1.00
186_A	190_A	0.957	1.00
207_L	211_L	0.952	1.00
55_L	59_A	0.947	1.00
29_L	33_F	0.942	1.00
34_F	145_L	0.938	1.00
96_F	99_I	0.937	1.00
44_Y	48_I	0.929	1.00
145_L	156_W	0.929	1.00
200_L	204_L	0.924	1.00
99_I	103_L	0.922	1.00
191_G	198_D	0.919	1.00
144_L	147_P	0.914	1.00
89_Q	93_L	0.907	1.00
187_A	190_A	0.902	1.00
125_L	129_A	0.901	1.00
168_V	172_L	0.900	1.00
10_L	13_A	0.896	1.00
98_N	101_A	0.891	1.00
77_Q	81_D	0.891	1.00
200_L	203_L	0.890	1.00
3_I	7_L	0.884	1.00
10_L	29_L	0.883	1.00
95_F	99_I	0.881	1.00
27_K	31_I	0.877	1.00
198_D	202_L	0.869	1.00
4_Y	8_A	0.863	1.00
41_W	55_L	0.858	1.00
17_I	23_E	0.858	1.00
8_A	27_K	0.856	1.00
32_G	35_L	0.854	1.00
118_I	121_A	0.853	1.00
158_G	162_S	0.853	1.00
103_L	107_L	0.852	1.00
11_R	14_L	0.852	1.00
47_I	51_S	0.844	1.00
40_N	44_Y	0.844	1.00
99_I	102_I	0.842	1.00
118_I	122_Q	0.836	1.00
179_T	182_D	0.835	1.00
30_K	150_R	0.833	1.00
36_A	39_T	0.833	1.00
137_G	141_I	0.828	1.00
198_D	201_A	0.828	1.00
8_A	11_R	0.827	1.00
9_G	12_L	0.825	1.00
32_G	36_A	0.823	1.00
165_L	168_V	0.820	1.00
42_P	45_A	0.811	1.00
164_G	167_L	0.802	1.00
11_R	26_K	0.801	1.00
106_L	110_L	0.801	1.00
155_G	162_S	0.797	1.00
108_A	112_V	0.790	1.00
142_P	151_F	0.789	1.00
208_V	211_L	0.786	1.00
204_L	208_V	0.783	1.00
95_F	98_N	0.780	1.00
91_S	94_S	0.779	1.00
31_I	35_L	0.778	1.00
110_L	114_L	0.776	1.00
43_A	46_T	0.774	1.00
129_A	159_A	0.774	1.00
211_L	214_I	0.772	1.00
184_F	188_L	0.771	1.00
122_Q	125_L	0.769	1.00
199_A	211_L	0.768	1.00
143_F	149_T	0.765	1.00
205_A	210_L	0.760	1.00
70_L	73_P	0.755	1.00
11_R	17_I	0.755	1.00
100_G	103_L	0.754	1.00
38_A	41_W	0.753	1.00
8_A	23_E	0.743	1.00
3_I	6_A	0.742	1.00
152_L	159_A	0.739	1.00
25_V	32_G	0.739	1.00
8_A	12_L	0.727	1.00
122_Q	170_L	0.724	1.00
62_A	65_G	0.724	1.00
60_A	70_L	0.721	1.00
11_R	27_K	0.718	1.00
197_A	206_A	0.717	1.00
27_K	30_K	0.712	1.00
51_S	56_G	0.709	1.00
60_A	64_L	0.706	1.00
136_L	140_F	0.706	1.00
201_A	208_V	0.705	1.00
114_L	118_I	0.703	1.00
208_V	212_L	0.702	1.00
116_F	120_A	0.701	1.00
182_D	186_A	0.699	1.00
126_A	167_L	0.694	0.99
79_G	112_V	0.692	0.99
84_D	197_A	0.689	0.99
4_Y	147_P	0.688	0.99
163_Y	166_K	0.687	0.99
88_D	91_S	0.685	0.99
58_E	62_A	0.683	0.99
55_L	63_I	0.681	0.99
197_A	202_L	0.680	0.99
83_A	109_W	0.678	0.99
206_A	210_L	0.675	0.99
59_A	168_V	0.674	0.99
203_L	206_A	0.673	0.99
119_A	122_Q	0.667	0.99
69_L	73_P	0.667	0.99
141_I	156_W	0.667	0.99
173_I	177_G	0.662	0.99
69_L	72_S	0.662	0.99
160_V	164_G	0.659	0.99
30_K	33_F	0.659	0.99
196_L	201_A	0.658	0.99
199_A	209_L	0.655	0.99
197_A	203_L	0.655	0.99
187_A	191_G	0.652	0.99
16_R	26_K	0.644	0.99
44_Y	47_I	0.643	0.99
67_A	70_L	0.640	0.99
19_E	22_A	0.639	0.99
199_A	210_L	0.635	0.99
52_F	55_L	0.634	0.99
197_A	208_V	0.633	0.99
83_A	87_L	0.629	0.99
199_A	204_L	0.626	0.99
5_I	12_L	0.622	0.99
115_A	210_L	0.620	0.99
201_A	204_L	0.620	0.99
109_W	112_V	0.619	0.99
35_L	38_A	0.617	0.99
196_L	203_L	0.616	0.99
15_G	19_E	0.613	0.99
118_I	123_L	0.611	0.99
200_L	205_A	0.610	0.99
145_L	152_L	0.607	0.99
6_A	14_L	0.603	0.99
97_G	100_G	0.602	0.99
199_A	203_L	0.601	0.99
76_D	84_D	0.600	0.98
195_T	198_D	0.600	0.98
188_L	197_A	0.595	0.98
177_G	180_L	0.588	0.98
16_R	30_K	0.586	0.98
42_P	46_T	0.586	0.98
96_F	100_G	0.582	0.98
97_G	101_A	0.581	0.98
152_L	161_L	0.581	0.98
209_L	213_L	0.580	0.98
79_G	84_D	0.579	0.98
97_G	106_L	0.578	0.98
44_Y	51_S	0.578	0.98
80_F	86_L	0.576	0.98
76_D	79_G	0.574	0.98
189_A	192_A	0.574	0.98
129_A	167_L	0.574	0.98
119_A	174_V	0.571	0.98
98_N	102_I	0.571	0.98
60_A	65_G	0.569	0.98
180_L	184_F	0.566	0.98
8_A	13_A	0.566	0.98
172_L	176_I	0.565	0.98
48_I	52_F	0.565	0.98
56_G	59_A	0.565	0.98
48_I	55_L	0.564	0.98
88_D	94_S	0.562	0.98
6_A	12_L	0.559	0.98
206_A	213_L	0.558	0.98
87_L	90_A	0.557	0.98
59_A	65_G	0.556	0.98
84_D	92_S	0.553	0.97
108_A	113_L	0.552	0.97
134_L	138_P	0.549	0.97
56_G	60_A	0.548	0.97
11_R	22_A	0.548	0.97
4_Y	146_F	0.546	0.97
130_L	138_P	0.542	0.97
131_A	172_L	0.538	0.97
83_A	86_L	0.538	0.97
183_S	186_A	0.535	0.97
201_A	207_L	0.535	0.97
126_A	163_Y	0.532	0.97
37_L	41_W	0.532	0.97
90_A	94_S	0.532	0.97
74_A	77_Q	0.527	0.97
56_G	61_G	0.527	0.97
204_L	207_L	0.526	0.97
144_L	150_R	0.525	0.97
122_Q	166_K	0.524	0.97
6_A	9_G	0.523	0.96
87_L	93_L	0.522	0.96
23_E	26_K	0.522	0.96
196_L	206_A	0.519	0.96
11_R	15_G	0.518	0.96
85_P	93_L	0.517	0.96
194_P	200_L	0.513	0.96
101_A	106_L	0.510	0.96
89_Q	94_S	0.508	0.96
81_D	88_D	0.507	0.96
18_G	22_A	0.505	0.96
198_D	203_L	0.503	0.96
33_F	36_A	0.503	0.96
20_P	23_E	0.502	0.96
5_I	31_I	0.500	0.95

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
3wu2Y	1	0.1296	3.6	0.925	Contact Map
3zdqA	2	0.338	1.4	0.94	Contact Map
2mc7A	1	0.1296	1.2	0.942	Contact Map
4pj0Y	1	0.1343	1	0.945	Contact Map
4a82A	2	0.3287	0.9	0.946	Contact Map
3rkoM	1	0.3102	0.8	0.948	Contact Map
2ifoA	8	0.0787	0.8	0.948	Contact Map
2ksdA	1	0.2639	0.7	0.95	Contact Map
4he8M	1	0.3009	0.7	0.95	Contact Map
2nwlA	3	0.3981	0.7	0.95	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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