TrbH - PFAM28P - GREMLIN Contacts

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TrbH - Conjugal transfer protein TrbH

PFAM:	PF07283	Sequences: VDASAIAGDMVSRLAELYPPAKTTFNLKQDTSDAFGTALEAALRGWGYAVVEDQKTDKAAKPEASAAAAPGLPLAYVVDQFDGQVLYRLSLYVGSQSLSRAYTVTNGGATPAGPWSRKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	119 (107)
Sequences:	606 (438)
Seq/√Len:	42.3
META:	0.703

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_D	102_Y	5.600	1.00
10_M	91_L	4.118	1.00
79_D	88_R	3.790	1.00
10_M	35_F	2.974	1.00
20_P	48_Y	2.897	1.00
48_Y	56_T	2.486	1.00
36_G	76_Y	2.406	1.00
11_V	48_Y	2.236	1.00
10_M	89_L	2.138	0.99
86_L	112_A	2.005	0.99
36_G	77_V	1.685	0.97
21_A	52_E	1.657	0.97
18_Y	79_D	1.565	0.96
23_T	72_L	1.489	0.94
50_V	78_V	1.433	0.93
33_D	36_G	1.431	0.93
24_T	49_A	1.423	0.93
26_N	73_P	1.418	0.93
23_T	33_D	1.387	0.92
105_T	114_P	1.383	0.92
34_A	38_A	1.377	0.91
14_L	74_L	1.376	0.91
7_A	13_R	1.368	0.91
32_S	114_P	1.296	0.89
5_A	92_Y	1.289	0.88
20_P	23_T	1.265	0.87
36_G	111_P	1.196	0.84
30_D	116_S	1.195	0.84
7_A	38_A	1.191	0.84
14_L	48_Y	1.186	0.84
96_Q	115_W	1.175	0.83
43_L	91_L	1.171	0.83
78_V	89_L	1.160	0.82
20_P	112_A	1.152	0.82
114_P	117_R	1.143	0.81
7_A	83_G	1.136	0.81
29_Q	77_V	1.124	0.80
43_L	47_G	1.106	0.79
13_R	16_E	1.081	0.78
100_R	111_P	1.068	0.77
10_M	115_W	1.068	0.77
36_G	94_G	1.060	0.76
58_K	61_K	1.060	0.76
58_K	89_L	1.059	0.76
26_N	49_A	1.051	0.76
19_P	76_Y	1.044	0.75
39_L	78_V	1.032	0.74
109_A	118_K	1.027	0.74
25_F	74_L	1.027	0.74
54_Q	57_D	1.025	0.74
74_L	112_A	1.022	0.74
72_L	80_Q	1.016	0.73
15_A	46_W	1.016	0.73
33_D	115_W	1.012	0.73
17_L	87_Y	1.011	0.73
36_G	39_L	1.007	0.72
105_T	108_G	1.006	0.72
6_I	91_L	1.004	0.72
6_I	89_L	1.001	0.72
48_Y	103_T	1.000	0.72
29_Q	33_D	0.997	0.72
40_E	52_E	0.979	0.70
87_Y	99_S	0.970	0.70
18_Y	98_L	0.967	0.69
18_Y	23_T	0.951	0.68
14_L	95_S	0.946	0.68
6_I	10_M	0.933	0.67
44_R	52_E	0.930	0.66
52_E	115_W	0.927	0.66
14_L	93_V	0.913	0.65
84_Q	97_S	0.903	0.64
94_G	102_Y	0.903	0.64
5_A	8_G	0.900	0.64
113_G	117_R	0.876	0.62
21_A	96_Q	0.865	0.61
25_F	93_V	0.857	0.60
10_M	13_R	0.843	0.59
55_K	58_K	0.836	0.58
33_D	40_E	0.829	0.57
85_V	94_G	0.825	0.57
26_N	71_G	0.824	0.57
28_K	98_L	0.823	0.57
73_P	94_G	0.821	0.57
7_A	11_V	0.820	0.57
51_V	116_S	0.800	0.55
24_T	105_T	0.794	0.54
8_G	15_A	0.775	0.52
40_E	86_L	0.768	0.52
94_G	97_S	0.768	0.52
18_Y	93_V	0.766	0.51
95_S	102_Y	0.766	0.51
7_A	61_K	0.761	0.51
4_S	114_P	0.757	0.51
30_D	54_Q	0.757	0.51
73_P	83_G	0.753	0.50
13_R	91_L	0.746	0.50
33_D	97_S	0.744	0.49
50_V	101_A	0.733	0.48
6_I	9_D	0.730	0.48
35_F	99_S	0.730	0.48
23_T	107_G	0.729	0.48
11_V	20_P	0.726	0.48
10_M	113_G	0.724	0.48
18_Y	96_Q	0.724	0.48
41_A	101_A	0.722	0.47
10_M	79_D	0.716	0.47
11_V	36_G	0.713	0.46
13_R	86_L	0.709	0.46
29_Q	39_L	0.704	0.46
56_T	61_K	0.694	0.45
37_T	84_Q	0.693	0.45
48_Y	98_L	0.681	0.43
52_E	99_S	0.663	0.42
7_A	81_F	0.659	0.41
27_L	104_V	0.659	0.41
49_A	75_A	0.657	0.41
19_P	33_D	0.641	0.40
81_F	99_S	0.640	0.40
76_Y	107_G	0.638	0.40
41_A	46_W	0.637	0.39
9_D	48_Y	0.636	0.39
86_L	92_Y	0.634	0.39
8_G	42_A	0.632	0.39
6_I	78_V	0.630	0.39
21_A	24_T	0.624	0.38
14_L	25_F	0.624	0.38
42_A	82_D	0.602	0.36
25_F	30_D	0.601	0.36
13_R	87_Y	0.601	0.36
37_T	102_Y	0.600	0.36
45_G	70_P	0.588	0.35
39_L	47_G	0.586	0.35
58_K	94_G	0.583	0.35
7_A	35_F	0.582	0.35
25_F	87_Y	0.577	0.34
17_L	98_L	0.572	0.34
44_R	79_D	0.570	0.34
4_S	8_G	0.570	0.34
101_A	106_N	0.570	0.34
22_K	32_S	0.568	0.33
44_R	100_R	0.560	0.33
81_F	104_V	0.557	0.33
14_L	24_T	0.556	0.32
56_T	59_A	0.556	0.32
49_A	74_L	0.552	0.32
17_L	93_V	0.544	0.31
6_I	35_F	0.544	0.31
32_S	54_Q	0.535	0.31
11_V	42_A	0.534	0.31
78_V	87_Y	0.533	0.31
55_K	112_A	0.529	0.30
27_L	51_V	0.524	0.30
40_E	93_V	0.521	0.30
16_E	50_V	0.521	0.30
21_A	25_F	0.518	0.29
11_V	43_L	0.512	0.29
75_A	101_A	0.508	0.29
72_L	103_T	0.507	0.29
58_K	79_D	0.504	0.28
12_S	48_Y	0.500	0.28

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
3p73A	1	0.4286	31.9	0.898	Contact Map
3it8D	1	0.4034	31	0.899	Contact Map
4l4vA	1	0.4202	30.2	0.899	Contact Map
4g59A	1	0.3193	29.8	0.899	Contact Map
1t7vA	1	0.4202	29.3	0.9	Contact Map
4lzpB	2	0.7563	26.1	0.902	Contact Map
4g43A	1	0.4118	24.9	0.904	Contact Map
3fruA	1	0.4286	20.5	0.907	Contact Map
2wy3A	1	0.4202	19.7	0.908	Contact Map
3d2uA	2	0.4034	18.2	0.909	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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