Gluconate_2-dh3 - PFAM28P - GREMLIN Contacts

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Gluconate_2-dh3 - Gluconate 2-dehydrogenase subunit 3

PFAM:	PF13618	Sequences: AEEAATLEALADRIIPADDTPGAKEAGVPEFIDRMLADCYLPEDQEAYRAGLAALDAEARKRFGKPFADLSPAQQDALLDALEAGKAAGPEGSPGAAFFNLLRDLTLEGYYTSPIGGGNRDLGWKLIGFPG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	131 (125)
Sequences:	34346 (22562)
Seq/√Len:	2018.0
META:	0.945

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_A	25_E	3.334	1.00
71_S	74_Q	2.576	1.00
48_Y	105_L	2.391	1.00
62_R	81_A	2.324	1.00
8_E	24_K	2.309	1.00
11_A	106_T	2.254	1.00
13_R	76_D	2.177	1.00
3_E	49_R	1.988	1.00
67_F	75_Q	1.929	1.00
27_G	30_E	1.915	1.00
58_E	62_R	1.914	1.00
76_D	80_D	1.909	1.00
9_A	75_Q	1.890	1.00
4_A	29_P	1.860	1.00
13_R	75_Q	1.843	1.00
8_E	29_P	1.841	1.00
46_E	50_A	1.806	1.00
72_P	76_D	1.803	1.00
114_P	118_G	1.779	1.00
63_F	74_Q	1.699	1.00
51_G	98_F	1.696	1.00
31_F	109_G	1.673	1.00
12_D	24_K	1.658	1.00
66_P	69_D	1.614	1.00
74_Q	77_A	1.534	1.00
24_K	29_P	1.481	1.00
4_A	33_D	1.469	1.00
10_L	102_L	1.457	1.00
60_R	66_P	1.435	1.00
3_E	53_A	1.405	1.00
15_I	110_Y	1.382	1.00
65_K	74_Q	1.348	1.00
63_F	70_L	1.335	1.00
11_A	29_P	1.314	1.00
65_K	69_D	1.276	1.00
56_D	68_A	1.263	1.00
13_R	79_L	1.262	1.00
11_A	32_I	1.260	1.00
72_P	75_Q	1.250	1.00
4_A	8_E	1.225	1.00
59_A	70_L	1.203	1.00
58_E	78_L	1.202	1.00
103_R	107_L	1.202	1.00
53_A	57_A	1.186	1.00
6_T	68_A	1.177	1.00
12_D	17_A	1.171	1.00
28_V	110_Y	1.162	1.00
33_D	37_A	1.160	1.00
80_D	83_E	1.154	1.00
111_Y	120_R	1.152	1.00
54_A	58_E	1.149	1.00
6_T	10_L	1.122	1.00
13_R	72_P	1.121	1.00
41_L	44_D	1.109	1.00
56_D	66_P	1.101	1.00
10_L	79_L	1.100	1.00
57_A	61_K	1.096	1.00
59_A	78_L	1.093	1.00
59_A	63_F	1.075	1.00
9_A	24_K	1.073	1.00
45_Q	49_R	1.069	1.00
40_Y	43_E	1.066	1.00
2_E	56_D	1.054	1.00
77_A	81_A	1.053	1.00
34_R	38_D	1.026	1.00
83_E	99_F	1.025	1.00
63_F	77_A	1.024	1.00
9_A	13_R	1.023	1.00
77_A	80_D	1.020	1.00
42_P	46_E	1.017	1.00
58_E	61_K	0.994	1.00
55_L	82_L	0.992	1.00
80_D	84_A	0.981	1.00
9_A	68_A	0.976	1.00
5_A	68_A	0.970	1.00
47_A	101_L	0.964	1.00
2_E	66_P	0.962	1.00
26_A	110_Y	0.960	1.00
87_A	90_P	0.955	1.00
65_K	70_L	0.955	1.00
50_A	53_A	0.954	1.00
54_A	57_A	0.945	1.00
11_A	28_V	0.939	1.00
115_I	119_N	0.920	1.00
12_D	25_E	0.911	1.00
27_G	120_R	0.906	1.00
55_L	78_L	0.904	1.00
105_L	108_E	0.903	1.00
30_E	34_R	0.899	1.00
17_A	22_G	0.899	1.00
6_T	56_D	0.899	1.00
4_A	30_E	0.892	1.00
28_V	109_G	0.882	1.00
2_E	68_A	0.880	1.00
100_N	104_D	0.877	1.00
14_I	103_R	0.872	1.00
31_F	108_E	0.865	1.00
113_S	116_G	0.864	1.00
89_G	92_G	0.862	1.00
6_T	52_L	0.852	1.00
36_L	48_Y	0.849	1.00
7_L	102_L	0.848	1.00
101_L	105_L	0.841	1.00
104_D	108_E	0.839	1.00
5_A	69_D	0.821	1.00
14_I	106_T	0.821	1.00
56_D	59_A	0.819	1.00
111_Y	116_G	0.817	1.00
114_P	119_N	0.815	1.00
123_G	126_L	0.811	1.00
5_A	8_E	0.802	1.00
58_E	81_A	0.795	1.00
54_A	95_G	0.794	1.00
90_P	93_S	0.794	1.00
73_A	77_A	0.793	1.00
22_G	25_E	0.784	1.00
62_R	77_A	0.779	1.00
50_A	54_A	0.769	1.00
44_D	101_L	0.740	1.00
3_E	56_D	0.732	1.00
99_F	103_R	0.722	1.00
48_Y	102_L	0.722	1.00
94_P	97_A	0.716	1.00
2_E	6_T	0.716	1.00
17_A	24_K	0.712	1.00
96_A	100_N	0.711	1.00
26_A	122_L	0.701	1.00
32_I	106_T	0.697	1.00
117_G	122_L	0.687	1.00
15_I	107_L	0.684	1.00
73_A	76_D	0.682	1.00
39_C	42_P	0.678	1.00
70_L	74_Q	0.677	1.00
81_A	86_K	0.674	1.00
2_E	5_A	0.664	1.00
107_L	111_Y	0.662	1.00
47_A	97_A	0.660	1.00
55_L	59_A	0.648	1.00
46_E	49_R	0.646	1.00
17_A	20_T	0.642	1.00
57_A	60_R	0.638	1.00
11_A	23_A	0.636	1.00
122_L	125_K	0.631	1.00
8_E	12_D	0.629	1.00
56_D	60_R	0.624	1.00
29_P	33_D	0.621	1.00
39_C	43_E	0.619	1.00
65_K	71_S	0.618	1.00
44_D	47_A	0.613	1.00
40_Y	44_D	0.611	1.00
88_A	92_G	0.610	1.00
85_G	96_A	0.610	1.00
12_D	22_G	0.610	1.00
10_L	55_L	0.602	1.00
101_L	104_D	0.602	1.00
60_R	64_G	0.601	1.00
35_M	38_D	0.594	1.00
8_E	30_E	0.591	1.00
83_E	103_R	0.584	1.00
114_P	117_G	0.581	1.00
6_T	9_A	0.579	1.00
36_L	40_Y	0.578	1.00
93_S	97_A	0.576	1.00
116_G	120_R	0.575	1.00
32_I	109_G	0.573	1.00
88_A	91_E	0.572	1.00
13_R	67_F	0.571	1.00
117_G	120_R	0.568	1.00
7_L	11_A	0.566	1.00
108_E	112_T	0.563	1.00
110_Y	116_G	0.563	1.00
90_P	94_P	0.561	1.00
116_G	119_N	0.559	1.00
55_L	102_L	0.544	1.00
8_E	11_A	0.542	1.00
81_A	85_G	0.542	1.00
43_E	46_E	0.537	1.00
7_L	32_I	0.535	1.00
35_M	108_E	0.532	1.00
120_R	124_W	0.530	1.00
15_I	106_T	0.527	1.00
51_G	55_L	0.527	1.00
110_Y	120_R	0.524	1.00
76_D	79_L	0.523	1.00
34_R	37_A	0.518	1.00
7_L	52_L	0.516	1.00
42_P	45_Q	0.510	1.00
118_G	124_W	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
1r6nA	1	0.4656	23.8	0.889	Contact Map
2jexA	1	0.4504	21.8	0.891	Contact Map
1tueB	1	0.5038	21	0.891	Contact Map
2nnuA	1	0.4733	17.5	0.895	Contact Map
3plsA	1	0.5115	17	0.896	Contact Map
3zg1A	2	0.6794	16.6	0.896	Contact Map
4rt7A	2	0.4427	8.2	0.91	Contact Map
3vw8A	1	0.4656	7.4	0.911	Contact Map
4ksaA	3	0.916	7.4	0.911	Contact Map
4ksfA	3	0.8626	7.3	0.912	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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