TraV - PFAM28P - GREMLIN Contacts

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TraV - Type IV conjugative transfer system lipoprotein (TraV)

PFAM:	PF09676	Sequences: SEFACKAPDGGKCMSVSGAYANAVAGNLPSQRKAVTADKPKLATTPGAAVSSAASGPAPAAGAPAPAAAAGYRDSLYRELAGLLEAPVTPPVPAGRPLRSPPRVMRVWIAPWEDADGDLHMPRYVYVVVDPGRW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (127)
Sequences:	1092 (917)
Seq/√Len:	81.4
META:	0.745

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_R	124_Y	2.963	1.00
99_R	128_V	2.920	1.00
28_L	31_Q	2.812	1.00
128_V	132_G	2.750	1.00
113_E	117_G	2.687	1.00
111_P	122_P	2.679	1.00
14_M	19_A	2.556	1.00
105_M	127_V	2.549	1.00
15_S	18_G	2.287	1.00
107_V	127_V	2.186	1.00
5_C	13_C	2.091	1.00
114_D	120_H	2.082	1.00
106_R	126_Y	2.032	1.00
102_P	119_L	1.937	1.00
53_A	58_A	1.813	1.00
99_R	102_P	1.782	1.00
121_M	126_Y	1.745	1.00
120_H	123_R	1.740	1.00
55_S	64_P	1.727	1.00
51_S	55_S	1.714	1.00
12_K	22_N	1.647	1.00
100_S	130_D	1.629	1.00
52_S	56_G	1.616	1.00
102_P	132_G	1.597	1.00
97_P	126_Y	1.566	1.00
66_P	69_A	1.516	0.99
19_A	110_A	1.516	0.99
54_A	62_G	1.504	0.99
23_A	128_V	1.467	0.99
59_P	65_A	1.443	0.99
19_A	23_A	1.436	0.99
18_G	22_N	1.406	0.99
120_H	128_V	1.396	0.99
16_V	100_S	1.391	0.99
15_S	113_E	1.351	0.99
11_G	14_M	1.338	0.99
102_P	128_V	1.309	0.98
99_R	117_G	1.302	0.98
101_P	104_V	1.286	0.98
55_S	58_A	1.279	0.98
4_A	8_P	1.257	0.98
118_D	127_V	1.244	0.98
62_G	69_A	1.242	0.98
14_M	22_N	1.220	0.97
64_P	70_A	1.214	0.97
107_V	112_W	1.207	0.97
35_V	56_G	1.182	0.97
109_I	123_R	1.181	0.97
63_A	66_P	1.165	0.97
112_W	120_H	1.140	0.96
99_R	113_E	1.135	0.96
128_V	131_P	1.102	0.95
102_P	112_W	1.101	0.95
110_A	120_H	1.095	0.95
68_A	77_Y	1.093	0.95
58_A	68_A	1.092	0.95
53_A	56_G	1.088	0.95
51_S	66_P	1.066	0.94
114_D	118_D	1.065	0.94
121_M	132_G	1.062	0.94
11_G	19_A	1.037	0.93
16_V	132_G	1.033	0.93
71_G	74_D	1.025	0.93
29_P	32_R	1.024	0.93
102_P	133_R	1.018	0.93
99_R	108_W	1.015	0.93
52_S	64_P	1.007	0.92
102_P	106_R	0.996	0.92
6_K	16_V	0.990	0.92
57_P	60_A	0.983	0.91
107_V	124_Y	0.972	0.91
14_M	18_G	0.953	0.90
61_A	65_A	0.951	0.90
7_A	10_G	0.948	0.90
51_S	54_A	0.918	0.88
108_W	124_Y	0.914	0.88
51_S	62_G	0.907	0.88
57_P	61_A	0.906	0.88
26_G	33_K	0.897	0.87
122_P	127_V	0.875	0.86
12_K	19_A	0.874	0.86
4_A	20_Y	0.871	0.86
12_K	16_V	0.871	0.86
1_S	25_A	0.861	0.85
58_A	63_A	0.857	0.85
51_S	57_P	0.847	0.84
62_G	66_P	0.846	0.84
117_G	132_G	0.845	0.84
76_L	80_L	0.844	0.84
105_M	132_G	0.842	0.84
11_G	112_W	0.841	0.84
112_W	132_G	0.840	0.83
48_A	51_S	0.840	0.83
28_L	32_R	0.836	0.83
81_A	84_L	0.827	0.83
1_S	32_R	0.825	0.82
84_L	88_V	0.818	0.82
52_S	59_P	0.816	0.82
54_A	71_G	0.810	0.81
64_P	68_A	0.807	0.81
58_A	64_P	0.802	0.81
21_A	25_A	0.801	0.80
51_S	65_A	0.795	0.80
68_A	75_S	0.793	0.80
17_S	21_A	0.792	0.80
108_W	112_W	0.782	0.79
1_S	9_D	0.781	0.79
17_S	23_A	0.777	0.78
57_P	67_A	0.776	0.78
17_S	126_Y	0.775	0.78
54_A	59_P	0.774	0.78
1_S	99_R	0.773	0.78
67_A	71_G	0.771	0.78
126_Y	132_G	0.758	0.77
106_R	119_L	0.757	0.77
7_A	132_G	0.755	0.76
104_V	127_V	0.734	0.74
25_A	123_R	0.734	0.74
12_K	120_H	0.727	0.74
109_I	125_V	0.720	0.73
54_A	63_A	0.720	0.73
118_D	125_V	0.716	0.73
121_M	127_V	0.713	0.72
56_G	64_P	0.708	0.72
113_E	128_V	0.702	0.71
127_V	132_G	0.694	0.70
112_W	123_R	0.694	0.70
45_T	49_A	0.686	0.69
47_G	55_S	0.684	0.69
85_E	88_V	0.675	0.68
83_L	88_V	0.673	0.68
48_A	59_P	0.669	0.67
15_S	22_N	0.669	0.67
63_A	70_A	0.667	0.67
84_L	89_T	0.667	0.67
53_A	63_A	0.665	0.67
15_S	99_R	0.661	0.66
78_R	81_A	0.659	0.66
60_A	64_P	0.657	0.66
52_S	60_A	0.656	0.66
104_V	123_R	0.645	0.65
110_A	123_R	0.643	0.64
30_S	125_V	0.638	0.64
82_G	89_T	0.637	0.64
105_M	124_Y	0.634	0.63
12_K	110_A	0.626	0.62
107_V	126_Y	0.619	0.61
61_A	66_P	0.612	0.61
103_R	125_V	0.602	0.59
108_W	121_M	0.584	0.57
22_N	132_G	0.581	0.57
100_S	121_M	0.578	0.56
111_P	121_M	0.576	0.56
121_M	124_Y	0.576	0.56
52_S	62_G	0.574	0.56
57_P	70_A	0.572	0.55
23_A	123_R	0.569	0.55
56_G	62_G	0.563	0.54
6_K	10_G	0.559	0.54
9_D	104_V	0.558	0.54
52_S	61_A	0.558	0.54
105_M	113_E	0.555	0.53
16_V	98_L	0.553	0.53
48_A	52_S	0.552	0.53
71_G	75_S	0.551	0.53
51_S	56_G	0.548	0.52
20_Y	102_P	0.547	0.52
11_G	20_Y	0.546	0.52
20_Y	98_L	0.545	0.52
3_F	105_M	0.544	0.52
80_L	85_E	0.543	0.52
4_A	121_M	0.536	0.51
55_S	59_P	0.535	0.51
17_S	26_G	0.534	0.50
61_A	64_P	0.533	0.50
50_V	55_S	0.524	0.49
76_L	79_E	0.524	0.49
20_Y	118_D	0.523	0.49
19_A	24_V	0.522	0.49
24_V	131_P	0.521	0.49
17_S	107_V	0.513	0.48
20_Y	105_M	0.512	0.48
86_A	89_T	0.510	0.47
98_L	103_R	0.509	0.47
44_T	53_A	0.507	0.47
28_L	33_K	0.506	0.47
99_R	132_G	0.505	0.47
55_S	68_A	0.502	0.46
27_N	31_Q	0.501	0.46
60_A	66_P	0.500	0.46

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
1xi7A	1	0.1343	4.1	0.925	Contact Map
3ic3A	4	0.3433	3.7	0.927	Contact Map
3afhA	1	0.2164	2.7	0.932	Contact Map
1ffyA	1	0.4254	2	0.936	Contact Map
1y7uA	5	0.2985	1.9	0.937	Contact Map
4ncpA	5	0.2985	1.8	0.938	Contact Map
2b9sA	1	0.9478	1.7	0.938	Contact Map
3bjkA	5	0.291	1.7	0.939	Contact Map
2dybA	1	0.306	1.6	0.94	Contact Map
2i71A	2	0.2463	1.5	0.941	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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