YJDB - BACSU - GREMLIN Contacts

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YJDB - Uncharacterized protein YjdB

UniProt:	O31643	Sequences: MNFKKTVVSALSISALALSVSGVASAHEINSTPTEVKNISISPTHVIKIQDYNLPLKVGETYSVKNNSATRYWTDNQKVAEVDQNGLVTAKSKGKATITLFKGTAVFGKVYVTVY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	115 (92)
Sequences:	2341 (2165)
Seq/√Len:	225.7

BACSU - YJDB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_P	87_L	3.107	1.00
62_Y	65_K	2.961	1.00
48_K	90_A	2.883	1.00
80_A	88_V	2.739	1.00
36_V	60_E	2.496	1.00
75_D	96_A	2.218	1.00
81_E	91_K	2.202	1.00
46_V	54_L	2.113	1.00
66_N	70_T	1.821	1.00
66_N	69_A	1.763	1.00
80_A	96_A	1.750	1.00
95_K	111_Y	1.747	1.00
82_V	88_V	1.682	1.00
75_D	99_T	1.666	1.00
56_L	88_V	1.664	1.00
83_D	87_L	1.642	1.00
74_T	77_Q	1.636	1.00
79_V	96_A	1.585	1.00
72_Y	100_L	1.534	1.00
70_T	100_L	1.530	1.00
47_I	113_T	1.527	1.00
73_W	101_F	1.500	1.00
38_N	61_T	1.463	1.00
50_Q	93_K	1.439	1.00
76_N	79_V	1.420	1.00
74_T	98_I	1.407	1.00
58_V	72_Y	1.399	1.00
41_I	110_V	1.386	1.00
43_P	46_V	1.372	1.00
97_T	111_Y	1.291	1.00
49_I	52_Y	1.284	1.00
43_P	110_V	1.266	1.00
40_S	61_T	1.250	1.00
80_A	98_I	1.223	1.00
82_V	86_G	1.174	1.00
56_L	82_V	1.147	1.00
53_N	89_T	1.140	1.00
75_D	97_T	1.127	1.00
102_K	105_A	1.095	1.00
36_V	65_K	1.093	1.00
79_V	114_V	1.082	1.00
99_T	107_F	1.075	1.00
27_H	31_S	1.074	1.00
97_T	109_K	1.072	1.00
74_T	82_V	1.063	1.00
50_Q	90_A	1.058	1.00
34_T	64_V	1.054	1.00
39_I	108_G	1.032	1.00
55_P	86_G	1.028	1.00
58_V	100_L	1.013	1.00
73_W	99_T	0.988	1.00
23_V	26_A	0.979	1.00
48_K	52_Y	0.975	1.00
36_V	62_Y	0.972	1.00
79_V	94_G	0.972	1.00
48_K	54_L	0.959	1.00
43_P	54_L	0.955	1.00
40_S	59_G	0.950	1.00
53_N	87_L	0.946	1.00
36_V	106_V	0.941	1.00
60_E	102_K	0.931	1.00
96_A	114_V	0.922	1.00
77_Q	81_E	0.917	1.00
69_A	103_G	0.911	0.99
95_K	113_T	0.891	0.99
74_T	80_A	0.889	0.99
71_R	101_F	0.875	0.99
46_V	112_V	0.874	0.99
100_L	108_G	0.837	0.99
41_I	108_G	0.834	0.99
56_L	72_Y	0.811	0.99
42_S	57_K	0.797	0.99
62_Y	102_K	0.797	0.99
105_A	108_G	0.781	0.98
34_T	63_S	0.743	0.98
62_Y	67_N	0.740	0.98
46_V	110_V	0.739	0.98
39_I	106_V	0.731	0.98
44_T	108_G	0.724	0.97
41_I	56_L	0.722	0.97
74_T	96_A	0.720	0.97
41_I	58_V	0.707	0.97
49_I	93_K	0.701	0.97
48_K	88_V	0.683	0.96
31_S	34_T	0.681	0.96
39_I	58_V	0.677	0.96
35_E	66_N	0.676	0.96
106_V	110_V	0.669	0.96
99_T	109_K	0.662	0.96
32_T	49_I	0.660	0.96
32_T	35_E	0.659	0.95
39_I	60_E	0.656	0.95
23_V	27_H	0.652	0.95
27_H	30_N	0.647	0.95
41_I	72_Y	0.644	0.95
60_E	66_N	0.642	0.95
67_N	103_G	0.636	0.95
24_A	31_S	0.633	0.94
75_D	78_K	0.624	0.94
32_T	52_Y	0.623	0.94
101_F	104_T	0.622	0.94
37_K	62_Y	0.621	0.94
108_G	112_V	0.620	0.94
101_F	107_F	0.618	0.94
60_E	65_K	0.616	0.94
25_S	30_N	0.616	0.94
56_L	110_V	0.606	0.93
35_E	63_S	0.603	0.93
82_V	96_A	0.601	0.93
74_T	79_V	0.597	0.92
50_Q	92_S	0.587	0.92
34_T	62_Y	0.585	0.92
79_V	92_S	0.579	0.91
28_E	31_S	0.579	0.91
74_T	86_G	0.574	0.91
84_Q	91_K	0.572	0.91
106_V	114_V	0.572	0.91
63_S	67_N	0.564	0.90
47_I	92_S	0.561	0.90
42_S	59_G	0.560	0.90
70_T	102_K	0.555	0.90
80_A	94_G	0.546	0.89
98_I	112_V	0.544	0.89
43_P	56_L	0.544	0.89
23_V	29_I	0.543	0.88
34_T	66_N	0.543	0.88
60_E	69_A	0.539	0.88
74_T	99_T	0.539	0.88
102_K	106_V	0.534	0.88
43_P	100_L	0.532	0.87
83_D	89_T	0.525	0.87
74_T	91_K	0.518	0.86
110_V	114_V	0.514	0.86
39_I	66_N	0.509	0.85
44_T	109_K	0.508	0.85
36_V	104_T	0.507	0.85
81_E	86_G	0.500	0.84
24_A	27_H	0.500	0.84

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
2l04A	1	0.7391	99.5	0.356	Contact Map
2mogA	1	0.7217	99.4	0.373	Contact Map
2mh4A	1	0.7217	99.4	0.383	Contact Map
3ncxA	1	0.7913	98.9	0.502	Contact Map
1f00I	1	0.9565	97.5	0.66	Contact Map
4aq1A	1	1	97	0.69	Contact Map
1f1sA	1	0.6435	96.1	0.718	Contact Map
2l7yA	1	0.6696	89.4	0.781	Contact Map
4r5oA	3	0.8	74.9	0.815	Contact Map
1cwvA	1	0.6957	72.8	0.819	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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