TrbI_Ftype - PFAM28P - GREMLIN Contacts

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TrbI_Ftype - Type-F conjugative transfer system protein (TrbI_Ftype)

PFAM:	PF09677	Sequences: WALVLALLAALLWGAWVTRLLLRLPQPRIVTVDLKGIVGEFVQALARSGLSPEQVKALTRRFMAALEAALQEYAARHGVVVLVAEAVVAGAPDITPEVRAAVARRM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	106 (101)
Sequences:	706 (547)
Seq/√Len:	54.4
META:	0.761

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_V	81_V	5.292	1.00
40_E	99_R	3.158	1.00
32_V	37_I	2.708	1.00
33_D	36_G	2.669	1.00
33_D	84_A	2.473	1.00
30_V	94_I	2.460	1.00
51_S	54_Q	2.259	1.00
73_Y	94_I	2.172	1.00
65_A	69_A	2.111	1.00
69_A	101_A	2.105	1.00
55_V	59_T	2.100	1.00
81_V	94_I	1.962	1.00
82_L	87_V	1.901	1.00
101_A	104_R	1.751	0.99
7_L	18_T	1.736	0.99
37_I	99_R	1.733	0.99
15_A	18_T	1.711	0.99
73_Y	77_H	1.604	0.98
35_K	39_G	1.537	0.98
56_K	60_R	1.502	0.97
83_V	88_V	1.491	0.97
74_A	79_V	1.486	0.97
39_G	88_V	1.484	0.97
69_A	98_V	1.471	0.97
11_L	15_A	1.425	0.96
41_F	62_F	1.423	0.96
61_R	65_A	1.393	0.96
5_L	10_A	1.342	0.95
4_V	7_L	1.323	0.95
96_P	99_R	1.302	0.94
34_L	83_V	1.292	0.94
41_F	65_A	1.275	0.93
74_A	89_A	1.222	0.92
17_V	21_L	1.201	0.91
4_V	10_A	1.198	0.91
22_L	25_P	1.194	0.91
83_V	86_A	1.191	0.91
70_L	81_V	1.165	0.90
66_L	80_V	1.154	0.89
32_V	73_Y	1.149	0.89
58_L	61_R	1.109	0.87
5_L	9_A	1.099	0.87
17_V	52_P	1.078	0.86
65_A	98_V	1.073	0.86
45_L	55_V	1.071	0.85
38_V	42_V	1.070	0.85
9_A	13_W	1.068	0.85
70_L	80_V	1.050	0.84
100_A	104_R	1.037	0.84
34_L	86_A	1.036	0.84
60_R	64_A	1.021	0.83
29_I	80_V	1.014	0.82
38_V	88_V	1.007	0.82
38_V	67_E	1.006	0.82
34_L	47_R	0.991	0.81
33_D	73_Y	0.991	0.81
7_L	10_A	0.991	0.81
57_A	78_G	0.944	0.77
37_I	40_E	0.939	0.77
31_T	90_G	0.938	0.77
88_V	91_A	0.929	0.76
92_P	97_E	0.917	0.75
31_T	84_A	0.916	0.75
29_I	36_G	0.916	0.75
17_V	20_L	0.899	0.74
40_E	44_A	0.888	0.73
13_W	18_T	0.887	0.73
23_R	60_R	0.874	0.72
67_E	71_Q	0.862	0.71
16_W	19_R	0.829	0.68
53_E	56_K	0.828	0.68
6_A	9_A	0.816	0.66
9_A	14_G	0.798	0.65
30_V	73_Y	0.797	0.65
62_F	66_L	0.787	0.64
29_I	38_V	0.787	0.64
59_T	63_M	0.786	0.64
54_Q	58_L	0.785	0.63
12_L	18_T	0.779	0.63
13_W	16_W	0.775	0.62
31_T	91_A	0.773	0.62
16_W	94_I	0.768	0.62
11_L	22_L	0.767	0.62
26_Q	30_V	0.753	0.60
39_G	58_L	0.746	0.59
41_F	94_I	0.744	0.59
22_L	68_A	0.738	0.59
18_T	23_R	0.738	0.59
33_D	85_E	0.736	0.58
8_L	11_L	0.732	0.58
16_W	22_L	0.695	0.54
85_E	88_V	0.693	0.54
29_I	41_F	0.692	0.54
47_R	70_L	0.692	0.54
35_K	38_V	0.689	0.53
35_K	41_F	0.682	0.53
56_K	79_V	0.681	0.53
30_V	61_R	0.681	0.53
49_G	88_V	0.672	0.52
28_R	54_Q	0.665	0.51
32_V	94_I	0.662	0.51
32_V	88_V	0.655	0.50
66_L	70_L	0.647	0.49
43_Q	47_R	0.641	0.48
68_A	72_E	0.638	0.48
41_F	45_L	0.633	0.47
28_R	92_P	0.628	0.47
32_V	63_M	0.622	0.46
74_A	90_G	0.619	0.46
38_V	55_V	0.608	0.45
60_R	70_L	0.604	0.44
59_T	67_E	0.599	0.44
51_S	73_Y	0.598	0.44
38_V	96_P	0.595	0.43
26_Q	78_G	0.589	0.43
42_V	52_P	0.579	0.42
51_S	55_V	0.578	0.42
79_V	83_V	0.576	0.41
4_V	11_L	0.574	0.41
7_L	66_L	0.573	0.41
49_G	52_P	0.569	0.41
47_R	51_S	0.567	0.41
59_T	89_A	0.564	0.40
31_T	89_A	0.562	0.40
71_Q	75_A	0.557	0.40
39_G	55_V	0.554	0.39
33_D	50_L	0.553	0.39
83_V	91_A	0.553	0.39
65_A	102_V	0.550	0.39
88_V	92_P	0.537	0.37
73_Y	79_V	0.536	0.37
63_M	66_L	0.536	0.37
72_E	101_A	0.535	0.37
52_P	56_K	0.534	0.37
68_A	76_R	0.534	0.37
8_L	100_A	0.533	0.37
69_A	102_V	0.528	0.37
85_E	95_T	0.528	0.37
71_Q	78_G	0.520	0.36
4_V	9_A	0.518	0.36
45_L	85_E	0.513	0.35
53_E	92_P	0.512	0.35
12_L	64_A	0.511	0.35
16_W	20_L	0.506	0.34
37_I	98_V	0.505	0.34
28_R	59_T	0.504	0.34
57_A	71_Q	0.504	0.34
66_L	82_L	0.503	0.34
42_V	84_A	0.503	0.34
64_A	101_A	0.502	0.34
41_F	63_M	0.501	0.34
37_I	54_Q	0.500	0.34

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
1u2mA	3	0.7547	94	0.765	Contact Map
4kqtA	1	0.8585	87.1	0.801	Contact Map
1scfA	4	0	27.5	0.872	Contact Map
3b09A	2	0.5094	11.9	0.891	Contact Map
2hsgA	1	0.3774	11.8	0.892	Contact Map
1qpzA	2	0.3679	10.5	0.894	Contact Map
4gycB	2	0.2075	8.8	0.898	Contact Map
3gcgB	1	0.6038	8.7	0.898	Contact Map
4ldfA	2	0.4717	8.1	0.899	Contact Map
2o20A	2	0	7.8	0.9	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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