TrbC_Ftype - PFAM28P - GREMLIN Contacts

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TrbC_Ftype - Type-F conjugative transfer system pilin assembly protein

PFAM:	PF09673	Sequences: VFVSFSMPEASLRRLARQAARAGAVLVLRGLVGGMSLKPTAKRIQELLGKEDRGVGVQIDPRLFRRFGITRVPAFVLVKGDAAPCAGGGCAAPPPFDKVYGDVSLDYALETI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	112 (110)
Sequences:	1858 (1420)
Seq/√Len:	135.4
META:	0.851

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_G	39_P	4.175	1.00
32_V	40_T	2.973	1.00
74_A	100_Y	2.747	1.00
3_V	12_L	2.643	1.00
15_L	75_F	2.494	1.00
103_V	107_Y	2.481	1.00
2_F	63_L	2.439	1.00
1_V	75_F	2.370	1.00
16_A	26_L	2.328	1.00
9_E	46_E	2.231	1.00
28_L	40_T	2.153	1.00
5_F	43_R	2.092	1.00
3_V	26_L	2.046	1.00
4_S	72_V	2.025	1.00
99_V	108_A	1.915	1.00
19_A	24_A	1.894	1.00
75_F	108_A	1.890	1.00
67_F	76_V	1.881	1.00
3_V	28_L	1.832	1.00
103_V	108_A	1.818	1.00
74_A	98_K	1.808	1.00
11_S	15_L	1.779	1.00
2_F	69_I	1.730	1.00
7_M	12_L	1.700	1.00
32_V	43_R	1.692	1.00
25_V	58_Q	1.658	1.00
31_L	37_L	1.564	1.00
97_D	102_D	1.527	1.00
2_F	76_V	1.429	1.00
39_P	42_K	1.416	1.00
3_V	7_M	1.403	1.00
36_S	39_P	1.348	1.00
11_S	102_D	1.319	1.00
9_E	43_R	1.312	1.00
69_I	74_A	1.254	1.00
76_V	98_K	1.240	1.00
19_A	26_L	1.223	1.00
9_E	13_R	1.221	1.00
45_Q	49_G	1.182	0.99
18_Q	106_D	1.149	0.99
5_F	32_V	1.147	0.99
104_S	107_Y	1.132	0.99
8_P	11_S	1.123	0.99
67_F	78_V	1.093	0.99
20_A	53_R	1.084	0.99
78_V	81_D	1.079	0.99
2_F	67_F	1.013	0.98
13_R	48_L	1.012	0.98
31_L	59_I	1.002	0.98
48_L	57_V	0.995	0.98
3_V	15_L	0.987	0.98
13_R	50_K	0.980	0.98
11_S	14_R	0.974	0.98
1_V	15_L	0.962	0.98
106_D	110_E	0.961	0.98
27_V	63_L	0.959	0.98
62_R	66_R	0.956	0.98
41_A	45_Q	0.946	0.97
20_A	54_G	0.942	0.97
14_R	102_D	0.935	0.97
16_A	55_V	0.934	0.97
76_V	96_F	0.932	0.97
87_G	93_P	0.926	0.97
44_I	57_V	0.912	0.97
89_G	93_P	0.897	0.97
85_C	90_C	0.893	0.96
37_L	40_T	0.892	0.96
99_V	111_T	0.881	0.96
8_P	102_D	0.872	0.96
33_G	36_S	0.853	0.95
42_K	45_Q	0.852	0.95
42_K	46_E	0.850	0.95
6_S	72_V	0.839	0.95
14_R	18_Q	0.830	0.95
18_Q	21_R	0.828	0.95
87_G	90_C	0.825	0.94
46_E	49_G	0.819	0.94
12_L	43_R	0.813	0.94
43_R	47_L	0.808	0.94
29_R	65_R	0.779	0.93
75_F	99_V	0.778	0.93
28_L	57_V	0.776	0.92
10_A	14_R	0.771	0.92
75_F	105_L	0.770	0.92
3_V	57_V	0.768	0.92
38_K	41_A	0.762	0.92
4_S	57_V	0.755	0.91
43_R	46_E	0.746	0.91
67_F	96_F	0.743	0.91
18_Q	22_A	0.740	0.91
91_A	95_P	0.739	0.90
87_G	91_A	0.730	0.90
88_G	92_A	0.729	0.90
38_K	42_K	0.727	0.90
2_F	64_F	0.723	0.90
31_L	36_S	0.718	0.89
5_F	28_L	0.711	0.89
90_C	93_P	0.706	0.88
12_L	16_A	0.703	0.88
1_V	108_A	0.703	0.88
96_F	109_L	0.681	0.87
5_F	33_G	0.680	0.86
12_L	28_L	0.663	0.85
20_A	42_K	0.660	0.85
72_V	91_A	0.657	0.85
66_R	79_K	0.652	0.84
1_V	105_L	0.649	0.84
67_F	109_L	0.648	0.84
48_L	53_R	0.641	0.83
58_Q	67_F	0.637	0.83
107_Y	111_T	0.635	0.83
47_L	63_L	0.635	0.83
13_R	59_I	0.635	0.83
33_G	43_R	0.632	0.82
77_L	102_D	0.631	0.82
58_Q	74_A	0.626	0.82
1_V	19_A	0.623	0.81
25_V	56_G	0.620	0.81
16_A	53_R	0.611	0.80
10_A	85_C	0.608	0.80
7_M	31_L	0.605	0.79
7_M	11_S	0.603	0.79
6_S	32_V	0.602	0.79
62_R	65_R	0.600	0.79
5_F	40_T	0.598	0.79
88_G	94_P	0.584	0.77
99_V	103_V	0.581	0.77
16_A	20_A	0.579	0.76
77_L	97_D	0.577	0.76
48_L	55_V	0.577	0.76
28_L	64_F	0.575	0.76
82_A	85_C	0.574	0.76
31_L	40_T	0.574	0.76
32_V	62_R	0.564	0.75
77_L	81_D	0.564	0.75
21_R	106_D	0.552	0.73
99_V	107_Y	0.549	0.73
31_L	34_G	0.545	0.72
16_A	48_L	0.544	0.72
89_G	94_P	0.541	0.71
28_L	32_V	0.541	0.71
15_L	102_D	0.540	0.71
68_G	89_G	0.539	0.71
69_I	98_K	0.538	0.71
102_D	105_L	0.536	0.71
75_F	102_D	0.536	0.71
17_R	53_R	0.533	0.70
34_G	57_V	0.531	0.70
1_V	26_L	0.525	0.69
92_A	95_P	0.524	0.69
102_D	107_Y	0.523	0.69
8_P	18_Q	0.522	0.69
89_G	92_A	0.516	0.68
22_A	109_L	0.515	0.68
33_G	40_T	0.514	0.68
28_L	43_R	0.511	0.67
97_D	109_L	0.511	0.67
91_A	94_P	0.510	0.67
16_A	47_L	0.509	0.67
20_A	23_G	0.508	0.67
5_F	15_L	0.507	0.67
89_G	95_P	0.507	0.67
15_L	27_V	0.502	0.66
42_K	59_I	0.501	0.66
73_P	101_G	0.500	0.65

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
4kcaA	2	0.8393	77.8	0.849	Contact Map
4hqzA	1	0.9018	66.5	0.861	Contact Map
3erwA	1	0.875	66	0.862	Contact Map
2hyxA	2	0.9018	65	0.863	Contact Map
3fw2A	2	0.8661	64.9	0.863	Contact Map
3hczA	2	0.8661	63.2	0.864	Contact Map
2es7A	1	0.75	62.7	0.864	Contact Map
3kcmA	1	0.875	62.3	0.865	Contact Map
4kcbA	1	0	61.2	0.866	Contact Map
1qmvA	3	0.8929	61.1	0.866	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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