Radical_SAM_C - PFAM28P - GREMLIN Contacts

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Radical_SAM_C - Radical_SAM C-terminal domain

PFAM:	PF16199	Sequences: PDGVKIHPLLVVKGTPLAKLYKRGEYKPLSLEEYVDLVADFLERLPPYIRIHRLTGDIPSELLVAGPWHPNLRQLIEKELKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	82 (80)
Sequences:	24223 (15839)
Seq/√Len:	1770.9
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_A	64_V	3.279	1.00
39_A	79_E	2.860	1.00
18_A	22_K	2.795	1.00
20_L	25_E	2.298	1.00
16_P	20_L	2.209	1.00
3_G	52_H	2.151	1.00
70_P	73_R	2.108	1.00
29_L	37_L	2.103	1.00
30_S	33_E	1.961	1.00
71_N	74_Q	1.767	1.00
19_K	23_R	1.668	1.00
28_P	65_A	1.659	1.00
36_D	79_E	1.588	1.00
31_L	35_V	1.524	1.00
8_P	69_H	1.512	1.00
9_L	17_L	1.503	1.00
6_I	41_F	1.496	1.00
13_K	18_A	1.485	1.00
45_L	51_I	1.454	1.00
46_P	49_I	1.418	1.00
40_D	44_R	1.406	1.00
16_P	19_K	1.370	1.00
59_P	62_L	1.370	1.00
40_D	43_E	1.313	1.00
13_K	64_V	1.292	1.00
42_L	51_I	1.284	1.00
11_V	26_Y	1.238	1.00
29_L	34_Y	1.230	1.00
42_L	45_L	1.214	1.00
19_K	22_K	1.206	1.00
8_P	55_T	1.205	1.00
42_L	77_E	1.157	1.00
13_K	22_K	1.156	1.00
39_A	43_E	1.110	1.00
35_V	39_A	1.043	1.00
31_L	73_R	1.042	1.00
36_D	39_A	1.032	1.00
34_Y	67_P	1.032	1.00
21_Y	65_A	1.029	1.00
37_L	41_F	1.013	1.00
11_V	18_A	1.003	1.00
21_Y	64_V	0.995	1.00
29_L	33_E	0.993	1.00
10_L	55_T	0.991	1.00
35_V	79_E	0.975	1.00
73_R	77_E	0.969	1.00
42_L	54_L	0.967	1.00
3_G	50_R	0.953	1.00
58_I	63_L	0.947	1.00
10_L	56_G	0.943	1.00
71_N	75_L	0.939	1.00
11_V	21_Y	0.934	1.00
17_L	20_L	0.933	1.00
60_S	70_P	0.931	1.00
6_I	38_V	0.920	1.00
20_L	23_R	0.920	1.00
37_L	40_D	0.915	1.00
1_P	4_V	0.895	1.00
4_V	44_R	0.892	1.00
69_H	75_L	0.859	1.00
31_L	68_W	0.851	1.00
41_F	44_R	0.841	1.00
72_L	75_L	0.808	1.00
4_V	51_I	0.807	1.00
12_V	58_I	0.790	1.00
35_V	76_I	0.787	1.00
12_V	15_T	0.777	1.00
39_A	80_L	0.770	1.00
60_S	63_L	0.761	1.00
18_A	21_Y	0.760	1.00
34_Y	38_V	0.753	1.00
70_P	74_Q	0.752	1.00
11_V	28_P	0.742	1.00
9_L	26_Y	0.733	1.00
58_I	62_L	0.729	1.00
20_L	24_G	0.725	1.00
8_P	56_G	0.722	1.00
74_Q	78_K	0.712	1.00
42_L	80_L	0.712	1.00
33_E	37_L	0.708	1.00
32_E	79_E	0.688	1.00
3_G	55_T	0.673	1.00
27_K	33_E	0.663	1.00
45_L	49_I	0.654	1.00
74_Q	77_E	0.648	1.00
7_H	56_G	0.643	1.00
21_Y	26_Y	0.627	1.00
22_K	64_V	0.626	1.00
11_V	17_L	0.621	1.00
2_D	50_R	0.615	1.00
39_A	76_I	0.610	1.00
31_L	67_P	0.606	1.00
12_V	63_L	0.606	1.00
10_L	69_H	0.606	1.00
54_L	76_I	0.604	1.00
1_P	49_I	0.603	1.00
36_D	40_D	0.600	1.00
52_H	55_T	0.600	1.00
63_L	66_G	0.599	1.00
43_E	47_P	0.584	1.00
42_L	76_I	0.584	1.00
30_S	34_Y	0.583	1.00
8_P	12_V	0.581	1.00
10_L	58_I	0.558	1.00
31_L	34_Y	0.558	1.00
22_K	25_E	0.554	1.00
76_I	80_L	0.553	1.00
12_V	62_L	0.545	1.00
2_D	49_I	0.542	1.00
31_L	69_H	0.540	1.00
33_E	36_D	0.538	1.00
6_I	51_I	0.535	1.00
10_L	63_L	0.531	1.00
30_S	65_A	0.529	1.00
21_Y	28_P	0.526	1.00
75_L	78_K	0.524	1.00
39_A	42_L	0.519	1.00
70_P	75_L	0.519	1.00
43_E	80_L	0.516	1.00
15_T	20_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
1r30A	2	0.9024	30.5	0.867	Contact Map
4wcxA	1	0.9268	16.7	0.882	Contact Map
3d0jA	2	0.561	13.9	0.887	Contact Map
4rtbA	2	0.9024	11.6	0.89	Contact Map
3iixA	1	0.9146	9.2	0.895	Contact Map
3t7vA	1	0.9024	8.5	0.897	Contact Map
1xdxA	2	0.6951	7.8	0.898	Contact Map
1oltA	1	0.9878	6.9	0.901	Contact Map
4mafA	2	0.5854	6.5	0.902	Contact Map
4g1gA	2	0.378	5.9	0.904	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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