TrbC - PFAM28P - GREMLIN Contacts

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TrbC - TrbC/VIRB2 family

PFAM:	PF04956	Sequences: MKKLKRKRRRLLLLLLLAALLLLLASPAFAQGSGGSPWETPLQNILTSLTGPVAKAIAVIAIIVAGLMLAFGRGSKRRLIGIVFGLAIAFGASSIVAWI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	99 (90)
Sequences:	11653 (7370)
Seq/√Len:	776.8
META:	0.862

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_A	86_L	4.600	1.00
40_T	44_N	2.637	1.00
64_V	68_M	2.486	1.00
65_A	82_I	2.479	1.00
78_R	81_G	2.416	1.00
69_L	76_K	2.344	1.00
43_Q	47_T	2.258	1.00
77_R	81_G	2.244	1.00
39_E	48_S	2.197	1.00
66_G	85_G	2.063	1.00
54_A	89_A	1.896	1.00
42_L	56_A	1.881	1.00
39_E	43_Q	1.805	1.00
43_Q	46_L	1.788	1.00
46_L	56_A	1.773	1.00
66_G	88_I	1.698	1.00
65_A	79_L	1.523	1.00
75_S	78_R	1.481	1.00
51_G	56_A	1.450	1.00
62_I	82_I	1.417	1.00
46_L	60_I	1.395	1.00
91_G	96_V	1.335	1.00
52_P	56_A	1.320	1.00
10_R	14_L	1.307	1.00
67_L	71_F	1.307	1.00
9_R	12_L	1.297	1.00
70_A	89_A	1.282	1.00
91_G	94_S	1.250	1.00
28_A	32_G	1.240	1.00
14_L	17_L	1.210	1.00
55_K	59_V	1.210	1.00
43_Q	56_A	1.204	1.00
66_G	89_A	1.202	1.00
68_M	78_R	1.165	1.00
28_A	31_Q	1.148	1.00
69_L	81_G	1.132	1.00
70_A	85_G	1.106	1.00
53_V	56_A	1.105	1.00
29_F	32_G	1.087	1.00
26_S	29_F	1.083	1.00
42_L	53_V	1.066	1.00
32_G	35_G	1.048	1.00
9_R	13_L	1.047	1.00
19_A	23_L	1.046	1.00
57_I	67_L	1.038	1.00
91_G	95_I	0.979	1.00
61_A	70_A	0.963	1.00
45_I	60_I	0.963	1.00
38_W	41_P	0.956	1.00
46_L	59_V	0.955	1.00
48_S	53_V	0.943	1.00
36_S	40_T	0.942	1.00
78_R	82_I	0.936	1.00
69_L	75_S	0.928	1.00
63_I	67_L	0.920	1.00
69_L	73_R	0.909	1.00
38_W	53_V	0.908	1.00
90_F	96_V	0.896	1.00
24_L	27_P	0.895	1.00
46_L	50_T	0.892	1.00
14_L	26_S	0.883	1.00
40_T	43_Q	0.866	1.00
17_L	22_L	0.864	1.00
11_L	14_L	0.862	1.00
38_W	48_S	0.850	1.00
12_L	15_L	0.842	1.00
25_A	28_A	0.826	1.00
11_L	15_L	0.826	1.00
22_L	30_A	0.825	1.00
25_A	29_F	0.824	1.00
17_L	20_L	0.817	1.00
10_R	13_L	0.812	1.00
65_A	74_G	0.809	1.00
81_G	84_F	0.791	1.00
68_M	74_G	0.771	1.00
61_A	82_I	0.769	1.00
46_L	93_S	0.767	1.00
20_L	24_L	0.750	1.00
58_A	91_G	0.744	1.00
12_L	16_L	0.738	1.00
31_Q	34_G	0.727	1.00
76_K	81_G	0.723	1.00
15_L	19_A	0.717	1.00
41_P	44_N	0.712	1.00
67_L	89_A	0.709	1.00
17_L	21_L	0.708	1.00
94_S	98_W	0.701	1.00
47_T	50_T	0.699	1.00
19_A	22_L	0.691	1.00
50_T	93_S	0.676	1.00
77_R	80_I	0.668	1.00
40_T	47_T	0.656	1.00
20_L	28_A	0.639	1.00
73_R	77_R	0.634	1.00
72_G	75_S	0.627	1.00
45_I	48_S	0.621	1.00
55_K	97_A	0.620	1.00
52_P	55_K	0.619	1.00
60_I	64_V	0.614	1.00
81_G	93_S	0.610	1.00
21_L	25_A	0.605	1.00
13_L	25_A	0.605	1.00
9_R	26_S	0.604	1.00
92_A	96_V	0.599	1.00
61_A	86_L	0.595	1.00
41_P	87_A	0.593	1.00
12_L	26_S	0.591	1.00
87_A	98_W	0.587	1.00
65_A	78_R	0.585	1.00
9_R	14_L	0.583	1.00
10_R	15_L	0.572	1.00
23_L	27_P	0.571	1.00
94_S	97_A	0.564	1.00
36_S	39_E	0.562	1.00
16_L	19_A	0.561	1.00
13_L	26_S	0.559	1.00
21_L	24_L	0.557	1.00
69_L	79_L	0.556	1.00
70_A	88_I	0.547	1.00
13_L	29_F	0.547	1.00
63_I	89_A	0.545	1.00
70_A	73_R	0.544	1.00
46_L	55_K	0.536	1.00
61_A	71_F	0.533	1.00
22_L	25_A	0.532	1.00
13_L	18_A	0.530	1.00
14_L	18_A	0.530	1.00
10_R	26_S	0.513	1.00
58_A	70_A	0.512	1.00
48_S	52_P	0.511	1.00
39_E	56_A	0.504	1.00
39_E	52_P	0.504	1.00
54_A	67_L	0.502	1.00
86_L	90_F	0.501	1.00
14_L	22_L	0.500	1.00

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
2wswA	3	0.9697	18.6	0.838	Contact Map
1fftB	1	0.7071	14.4	0.846	Contact Map
4px7A	1	0.9091	6	0.87	Contact Map
4ev6A	3	0.6768	5.4	0.873	Contact Map
2wh6A	1	0.8788	4.2	0.88	Contact Map
4i0uA	4	0.6566	4	0.881	Contact Map
4qi1A	3	0.9091	3.3	0.886	Contact Map
3qapA	1	0.9091	3.3	0.886	Contact Map
4fbzA	3	0.9091	3.3	0.886	Contact Map
4gc0A	1	0.9293	3.2	0.886	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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