YodL - PFAM28P - GREMLIN Contacts

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YodL - YodL-like

PFAM:	PF14191	Sequences: KFAIYQLKDDVDETRDYRFESLDELEKAGLEVDRENYELVYTGPLDDGETLEDIYEKFNIDHPADFKGHSLSVSDVVVLKQDGEVTAYYVDSFGFKELPEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	101 (99)
Sequences:	2089 (1572)
Seq/√Len:	158.0
META:	0.929

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_E	24_E	3.352	1.00
56_E	60_I	2.689	1.00
78_V	87_A	2.662	1.00
80_K	85_V	2.532	1.00
66_F	69_H	2.399	1.00
8_K	38_E	2.261	1.00
3_A	39_L	2.223	1.00
54_I	71_L	2.091	1.00
39_L	42_T	2.008	1.00
71_L	77_V	1.953	1.00
86_T	97_E	1.934	1.00
24_E	28_A	1.852	1.00
3_A	85_V	1.747	1.00
17_Y	36_N	1.692	1.00
59_N	70_S	1.679	1.00
22_L	96_K	1.668	1.00
90_V	95_F	1.626	1.00
21_S	24_E	1.618	1.00
10_D	13_E	1.564	1.00
56_E	61_D	1.552	1.00
7_L	14_T	1.540	1.00
53_D	56_E	1.538	1.00
18_R	69_H	1.474	1.00
55_Y	59_N	1.456	1.00
17_Y	30_L	1.432	1.00
4_I	58_F	1.427	1.00
57_K	61_D	1.400	1.00
25_L	89_Y	1.397	1.00
49_E	53_D	1.394	1.00
51_L	88_Y	1.331	1.00
73_V	92_S	1.316	1.00
41_Y	65_D	1.297	1.00
2_F	43_G	1.289	1.00
3_A	42_T	1.271	1.00
58_F	66_F	1.257	1.00
2_F	54_I	1.241	1.00
41_Y	63_P	1.237	1.00
3_A	78_V	1.234	1.00
74_S	89_Y	1.191	1.00
51_L	79_L	1.191	1.00
81_Q	84_E	1.175	1.00
22_L	26_E	1.158	1.00
20_E	28_A	1.146	1.00
33_D	36_N	1.140	1.00
2_F	45_L	1.133	1.00
50_T	53_D	1.132	1.00
25_L	32_V	1.116	1.00
3_A	80_K	1.092	0.99
45_L	50_T	1.086	0.99
4_I	77_V	1.080	0.99
88_Y	97_E	1.079	0.99
22_L	32_V	1.073	0.99
4_I	71_L	1.050	0.99
19_F	72_S	1.006	0.99
53_D	57_K	1.006	0.99
2_F	57_K	1.004	0.99
41_Y	58_F	0.988	0.99
7_L	36_N	0.983	0.99
9_D	18_R	0.967	0.99
17_Y	25_L	0.932	0.98
54_I	79_L	0.931	0.98
78_V	85_V	0.931	0.98
62_H	66_F	0.929	0.98
19_F	74_S	0.907	0.98
93_F	96_K	0.903	0.98
59_N	72_S	0.891	0.98
46_D	49_E	0.884	0.98
55_Y	70_S	0.883	0.98
32_V	36_N	0.882	0.98
58_F	68_G	0.879	0.98
52_E	77_V	0.879	0.98
52_E	56_E	0.874	0.97
52_E	90_V	0.871	0.97
21_S	27_K	0.871	0.97
34_R	39_L	0.857	0.97
59_N	62_H	0.834	0.97
8_K	12_D	0.832	0.97
45_L	57_K	0.816	0.96
23_D	26_E	0.806	0.96
40_V	68_G	0.804	0.96
63_P	66_F	0.802	0.96
45_L	48_G	0.800	0.96
20_E	25_L	0.797	0.96
5_Y	39_L	0.794	0.96
47_D	50_T	0.776	0.95
48_G	52_E	0.766	0.95
50_T	54_I	0.758	0.94
97_E	100_E	0.758	0.94
65_D	68_G	0.756	0.94
7_L	16_D	0.742	0.94
9_D	14_T	0.715	0.92
51_L	77_V	0.710	0.92
6_Q	72_S	0.710	0.92
14_T	17_Y	0.708	0.92
43_G	54_I	0.680	0.90
43_G	57_K	0.680	0.90
3_A	34_R	0.670	0.90
46_D	50_T	0.645	0.88
10_D	14_T	0.644	0.88
49_E	61_D	0.636	0.87
52_E	93_F	0.631	0.87
22_L	95_F	0.626	0.86
28_A	98_L	0.624	0.86
13_E	36_N	0.624	0.86
14_T	20_E	0.621	0.86
7_L	10_D	0.618	0.86
6_Q	68_G	0.618	0.86
22_L	25_L	0.611	0.85
69_H	72_S	0.599	0.84
17_Y	32_V	0.595	0.83
21_S	91_D	0.586	0.83
37_Y	74_S	0.584	0.82
14_T	36_N	0.581	0.82
24_E	27_K	0.579	0.82
47_D	81_Q	0.572	0.81
7_L	69_H	0.572	0.81
17_Y	29_G	0.571	0.81
40_V	69_H	0.566	0.80
72_S	93_F	0.566	0.80
5_Y	17_Y	0.559	0.79
23_D	28_A	0.552	0.79
52_E	95_F	0.551	0.79
76_V	98_L	0.551	0.79
49_E	99_P	0.548	0.78
4_I	66_F	0.542	0.77
5_Y	34_R	0.540	0.77
55_Y	62_H	0.537	0.77
23_D	27_K	0.537	0.77
45_L	81_Q	0.536	0.77
19_F	69_H	0.533	0.76
58_F	74_S	0.532	0.76
64_A	67_K	0.532	0.76
21_S	89_Y	0.529	0.76
79_L	86_T	0.529	0.76
74_S	91_D	0.527	0.75
82_D	85_V	0.525	0.75
62_H	70_S	0.524	0.75
42_T	81_Q	0.518	0.74
7_L	18_R	0.518	0.74
4_I	62_H	0.516	0.74
7_L	15_R	0.515	0.74
70_S	90_V	0.514	0.74
21_S	28_A	0.511	0.73
49_E	57_K	0.509	0.73
4_I	40_V	0.503	0.72
17_Y	20_E	0.500	0.72
7_L	13_E	0.500	0.72
12_D	28_A	0.500	0.72

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
4nazA	2	0.3465	6.5	0.917	Contact Map
1nnvA	1	0.7327	5.7	0.919	Contact Map
1v1cA	1	0.5149	5.5	0.92	Contact Map
4z04A	2	0.3168	5.5	0.92	Contact Map
3r4qA	2	0.3465	4.8	0.922	Contact Map
3g12A	2	0.3168	4.6	0.923	Contact Map
1u7iA	2	0.3366	4.5	0.924	Contact Map
2bjqA	1	0.7426	4.4	0.924	Contact Map
3uj4A	1	0.3168	4.1	0.925	Contact Map
2qntA	2	0.3762	3.9	0.926	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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