YGGT - PFAM28P - GREMLIN Contacts

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YGGT - YGGT family

PFAM:	PF02325	Sequences: NTLLGLYILLIIARAILSWRADPYNPIVRFLYRLTEPLLRPIRRILPLGGLDLSPLVAILLLQLLQRLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (67)
Sequences:	52169 (30811)
Seq/√Len:	3764.1
META:	0.924

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	35_T	2.400	1.00
36_E	40_R	2.045	1.00
38_L	41_P	2.026	1.00
4_L	66_Q	1.946	1.00
29_R	33_R	1.944	1.00
17_L	28_V	1.875	1.00
41_P	45_I	1.826	1.00
42_I	58_A	1.764	1.00
32_Y	36_E	1.749	1.00
10_L	35_T	1.720	1.00
63_Q	66_Q	1.709	1.00
38_L	58_A	1.660	1.00
5_G	9_L	1.619	1.00
8_I	63_Q	1.583	1.00
7_Y	38_L	1.576	1.00
5_G	66_Q	1.552	1.00
4_L	62_L	1.480	1.00
56_L	63_Q	1.413	1.00
15_A	55_P	1.413	1.00
14_R	36_E	1.386	1.00
36_E	43_R	1.383	1.00
63_Q	67_R	1.361	1.00
11_I	55_P	1.361	1.00
14_R	32_Y	1.327	1.00
22_D	25_N	1.285	1.00
42_I	61_L	1.272	1.00
8_I	66_Q	1.236	1.00
9_L	13_A	1.210	1.00
14_R	39_L	1.206	1.00
26_P	29_R	1.194	1.00
8_I	59_I	1.170	1.00
38_L	42_I	1.166	1.00
20_R	23_P	1.154	1.00
5_G	8_I	1.140	1.00
11_I	58_A	1.128	1.00
30_F	34_L	1.085	1.00
43_R	52_D	1.077	1.00
10_L	34_L	1.069	1.00
49_G	53_L	1.039	1.00
15_A	19_W	1.018	1.00
28_V	32_Y	1.004	1.00
59_I	63_Q	0.985	1.00
21_A	24_Y	0.977	1.00
52_D	55_P	0.955	1.00
22_D	26_P	0.955	1.00
34_L	37_P	0.954	1.00
48_L	53_L	0.932	1.00
13_A	31_L	0.906	1.00
25_N	28_V	0.903	1.00
39_L	55_P	0.896	1.00
39_L	58_A	0.894	1.00
2_T	6_L	0.894	1.00
4_L	8_I	0.880	1.00
25_N	29_R	0.852	1.00
27_I	30_F	0.794	1.00
42_I	45_I	0.736	1.00
12_I	59_I	0.735	1.00
42_I	57_V	0.733	1.00
5_G	63_Q	0.714	1.00
18_S	52_D	0.710	1.00
35_T	58_A	0.691	1.00
60_L	64_L	0.689	1.00
60_L	63_Q	0.684	1.00
24_Y	28_V	0.682	1.00
40_R	43_R	0.681	1.00
64_L	67_R	0.674	1.00
12_I	16_I	0.673	1.00
41_P	44_R	0.671	1.00
2_T	5_G	0.665	1.00
24_Y	27_I	0.663	1.00
21_A	26_P	0.653	1.00
62_L	66_Q	0.653	1.00
28_V	31_L	0.649	1.00
14_R	31_L	0.645	1.00
21_A	25_N	0.645	1.00
40_R	44_R	0.638	1.00
35_T	39_L	0.638	1.00
20_R	28_V	0.638	1.00
30_F	33_R	0.626	1.00
22_D	29_R	0.620	1.00
58_A	62_L	0.611	1.00
7_Y	62_L	0.610	1.00
42_I	54_S	0.582	1.00
12_I	15_A	0.573	1.00
46_L	57_V	0.565	1.00
24_Y	29_R	0.563	1.00
23_P	28_V	0.562	1.00
32_Y	35_T	0.561	1.00
39_L	54_S	0.546	1.00
15_A	18_S	0.545	1.00
57_V	61_L	0.533	1.00
21_A	28_V	0.528	1.00
61_L	65_L	0.523	1.00
42_I	46_L	0.517	1.00
23_P	29_R	0.512	1.00
64_L	68_L	0.504	1.00
15_A	56_L	0.503	1.00
6_L	10_L	0.503	1.00
20_R	25_N	0.501	1.00
11_I	39_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
1ku5A	2	0.5072	2.3	0.867	Contact Map
2nwlA	3	1	1.9	0.871	Contact Map
3duzA	3	0	1.8	0.873	Contact Map
1nmbN	1	0	1.8	0.874	Contact Map
3tiaA	3	0	1.8	0.874	Contact Map
2ls4A	1	0.3043	1.4	0.882	Contact Map
4b7jA	3	0	1.3	0.884	Contact Map
3s79A	1	0	1.2	0.885	Contact Map
3zdqA	2	0.4638	1.1	0.889	Contact Map
4l6vF	1	0.3768	0.8	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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