TfuA - PFAM28P - GREMLIN Contacts

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TfuA - TfuA-like protein

PFAM:	PF07812	Sequences: DGYFEQVPAVWHKEILWALSRGVHVFGAASMGALRAAELAPFGMIGVGRIFEAYRDGVLEDDDEVAVLHGPAELGYRPLSEALVNIRATLAAAVRAGVISAAEAAALLAAAKALFYPERT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (120)
Sequences:	4174 (3107)
Seq/√Len:	283.7
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
40_A	51_F	3.298	1.00
64_E	87_R	2.930	1.00
46_G	51_F	2.916	1.00
94_V	104_A	2.883	1.00
24_H	45_I	2.679	1.00
53_A	58_V	2.416	1.00
70_G	77_R	2.346	1.00
49_R	53_A	2.315	1.00
70_G	74_L	2.218	1.00
71_P	74_L	2.196	1.00
90_L	104_A	2.110	1.00
61_D	112_K	2.085	1.00
40_A	55_R	2.066	1.00
92_A	96_A	2.021	1.00
26_F	45_I	1.901	1.00
3_Y	7_V	1.739	1.00
68_L	80_S	1.708	1.00
86_I	90_L	1.672	1.00
52_E	56_D	1.621	1.00
5_E	116_Y	1.598	1.00
49_R	52_E	1.574	1.00
67_V	82_A	1.555	1.00
49_R	88_A	1.551	1.00
37_A	40_A	1.515	1.00
100_S	103_E	1.514	1.00
39_L	44_M	1.488	1.00
74_L	77_R	1.483	1.00
93_A	98_V	1.437	1.00
5_E	117_P	1.425	1.00
90_L	108_L	1.407	1.00
19_L	44_M	1.399	1.00
94_V	101_A	1.346	1.00
83_L	112_K	1.335	1.00
61_D	83_L	1.314	1.00
54_Y	59_L	1.272	1.00
104_A	108_L	1.241	1.00
17_W	20_S	1.239	1.00
68_L	117_P	1.236	1.00
63_D	112_K	1.227	1.00
68_L	79_L	1.224	1.00
13_K	16_L	1.218	1.00
59_L	84_V	1.188	1.00
3_Y	69_H	1.186	1.00
106_A	110_A	1.176	1.00
15_I	25_V	1.174	1.00
82_A	85_N	1.172	1.00
3_Y	6_Q	1.169	1.00
90_L	107_L	1.153	1.00
70_G	75_G	1.138	1.00
81_E	85_N	1.136	1.00
26_F	47_V	1.133	1.00
17_W	21_R	1.133	1.00
67_V	78_P	1.129	1.00
101_A	105_A	1.118	1.00
80_S	117_P	1.114	1.00
110_A	114_L	1.103	1.00
111_A	114_L	1.076	1.00
83_L	111_A	1.066	1.00
86_I	89_T	1.054	1.00
11_W	18_A	1.052	1.00
88_A	92_A	1.048	1.00
92_A	95_R	1.044	1.00
9_A	31_M	1.042	1.00
70_G	79_L	1.021	1.00
84_V	88_A	1.011	1.00
99_I	103_E	1.003	1.00
53_A	88_A	0.986	1.00
51_F	55_R	0.980	1.00
99_I	104_A	0.960	1.00
59_L	87_R	0.956	1.00
61_D	64_E	0.956	1.00
109_A	113_A	0.955	1.00
69_H	76_Y	0.951	1.00
18_A	25_V	0.944	1.00
5_E	11_W	0.936	1.00
53_A	59_L	0.934	1.00
81_E	86_I	0.921	1.00
64_E	108_L	0.910	1.00
28_A	47_V	0.900	1.00
59_L	64_E	0.888	1.00
88_A	91_A	0.887	1.00
83_L	108_L	0.881	1.00
53_A	91_A	0.853	1.00
13_K	17_W	0.847	1.00
89_T	92_A	0.847	1.00
8_P	12_H	0.843	1.00
16_L	42_F	0.832	1.00
105_A	109_A	0.830	1.00
54_Y	65_V	0.826	1.00
64_E	83_L	0.823	1.00
115_F	118_E	0.820	1.00
36_A	46_G	0.819	1.00
31_M	65_V	0.818	1.00
63_D	83_L	0.788	0.99
94_V	99_I	0.783	0.99
10_V	31_M	0.776	0.99
111_A	115_F	0.774	0.99
102_A	105_A	0.772	0.99
15_I	44_M	0.763	0.99
94_V	105_A	0.759	0.99
87_R	108_L	0.758	0.99
87_R	112_K	0.755	0.99
91_A	104_A	0.745	0.99
19_L	24_H	0.745	0.99
8_P	39_L	0.737	0.99
4_F	10_V	0.734	0.99
8_P	11_W	0.726	0.99
4_F	66_A	0.726	0.99
5_E	8_P	0.723	0.99
86_I	111_A	0.716	0.99
105_A	108_L	0.715	0.99
91_A	95_R	0.702	0.98
45_I	49_R	0.702	0.98
18_A	23_V	0.700	0.98
53_A	57_G	0.699	0.98
38_E	62_D	0.694	0.98
46_G	55_R	0.679	0.98
6_Q	9_A	0.678	0.98
12_H	17_W	0.677	0.98
114_L	118_E	0.675	0.98
72_A	76_Y	0.668	0.98
4_F	9_A	0.666	0.98
31_M	66_A	0.662	0.98
3_Y	13_K	0.658	0.98
107_L	110_A	0.657	0.98
55_R	58_V	0.654	0.98
50_I	84_V	0.654	0.98
94_V	100_S	0.647	0.97
19_L	25_V	0.640	0.97
12_H	16_L	0.636	0.97
39_L	42_F	0.635	0.97
97_G	101_A	0.635	0.97
83_L	86_I	0.635	0.97
110_A	113_A	0.634	0.97
106_A	109_A	0.612	0.96
70_G	73_E	0.611	0.96
91_A	108_L	0.604	0.96
93_A	96_A	0.600	0.96
11_W	17_W	0.600	0.96
18_A	61_D	0.599	0.96
74_L	79_L	0.595	0.96
54_Y	64_E	0.590	0.96
86_I	120_T	0.590	0.96
79_L	82_A	0.587	0.96
106_A	113_A	0.587	0.96
8_P	13_K	0.586	0.95
96_A	109_A	0.584	0.95
5_E	13_K	0.583	0.95
53_A	64_E	0.582	0.95
64_E	112_K	0.580	0.95
28_A	34_L	0.580	0.95
114_L	117_P	0.578	0.95
108_L	112_K	0.577	0.95
12_H	15_I	0.574	0.95
63_D	86_I	0.572	0.95
67_V	81_E	0.570	0.95
49_R	91_A	0.568	0.95
52_E	55_R	0.566	0.95
16_L	39_L	0.561	0.94
52_E	95_R	0.557	0.94
103_E	106_A	0.551	0.94
4_F	29_A	0.551	0.94
6_Q	82_A	0.549	0.94
35_R	62_D	0.548	0.94
99_I	107_L	0.548	0.94
76_Y	82_A	0.548	0.94
18_A	21_R	0.541	0.93
102_A	106_A	0.535	0.93
101_A	109_A	0.535	0.93
37_A	55_R	0.534	0.93
19_L	39_L	0.533	0.93
69_H	82_A	0.531	0.93
85_N	89_T	0.518	0.92
4_F	8_P	0.511	0.91
5_E	115_F	0.507	0.91
100_S	106_A	0.506	0.91
110_A	120_T	0.505	0.91
63_D	93_A	0.505	0.91
53_A	87_R	0.504	0.90
20_S	24_H	0.500	0.90

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
4gq4A	1	0.7333	28.4	0.928	Contact Map
2lwjA	1	0.7167	17.7	0.935	Contact Map
1uj8A	1	0.6083	15.4	0.937	Contact Map
3ohsX	2	0.8167	14.8	0.937	Contact Map
4i5lC	1	0.3583	13.7	0.938	Contact Map
3c8tA	4	0.5167	11.4	0.94	Contact Map
4l5gA	1	0.6917	11.1	0.94	Contact Map
2ou3A	2	0.55	9.7	0.942	Contact Map
4n18A	2	0.9083	9	0.943	Contact Map
3ip3A	2	0.9167	7.7	0.945	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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