DUF3744 - PFAM28P - GREMLIN Contacts

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DUF3744 - ATP-binding cassette cobalt transporter

PFAM:	PF12558	Sequences: SDLLKENGIREPLYITALKYAGVDITPEMHPSHIDTLDLSEDKEKLREWFESVPPPEKKPEKEPLLEVENLSF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (73)
Sequences:	1387 (1161)
Seq/√Len:	135.9
META:	0.727

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_V	71_L	5.157	1.00
64_P	67_E	3.863	1.00
2_D	6_E	3.254	1.00
11_E	19_K	2.591	1.00
44_E	48_E	2.586	1.00
9_I	16_T	2.125	1.00
18_L	37_L	2.010	1.00
46_L	50_F	1.879	1.00
23_V	42_D	1.796	1.00
8_G	16_T	1.776	1.00
3_L	7_N	1.701	1.00
25_I	31_P	1.668	1.00
39_L	42_D	1.656	1.00
10_R	13_L	1.549	1.00
27_P	31_P	1.517	1.00
29_M	42_D	1.513	1.00
43_K	47_R	1.507	1.00
30_H	36_T	1.329	1.00
32_S	36_T	1.307	1.00
18_L	23_V	1.280	1.00
28_E	31_P	1.268	1.00
44_E	47_R	1.247	1.00
48_E	52_S	1.238	1.00
5_K	9_I	1.210	1.00
15_I	32_S	1.203	1.00
46_L	49_W	1.184	0.99
23_V	46_L	1.166	0.99
18_L	46_L	1.155	0.99
4_L	9_I	1.153	0.99
19_K	34_I	1.143	0.99
45_K	48_E	1.123	0.99
15_I	33_H	1.121	0.99
17_A	21_A	1.065	0.99
38_D	42_D	1.041	0.99
30_H	38_D	1.026	0.99
57_E	60_P	1.018	0.98
16_T	20_Y	0.985	0.98
11_E	16_T	0.979	0.98
15_I	31_P	0.948	0.98
42_D	45_K	0.926	0.97
38_D	41_E	0.902	0.97
31_P	36_T	0.901	0.97
24_D	28_E	0.893	0.96
24_D	45_K	0.869	0.96
16_T	21_A	0.863	0.96
17_A	46_L	0.847	0.95
55_P	60_P	0.846	0.95
5_K	19_K	0.832	0.95
33_H	36_T	0.832	0.95
33_H	68_V	0.814	0.94
42_D	46_L	0.797	0.93
5_K	11_E	0.785	0.93
58_K	61_E	0.782	0.93
38_D	44_E	0.781	0.93
38_D	56_P	0.779	0.93
13_L	73_F	0.769	0.92
54_P	61_E	0.759	0.92
25_I	29_M	0.743	0.91
10_R	17_A	0.728	0.90
24_D	29_M	0.726	0.90
4_L	17_A	0.719	0.89
66_L	71_L	0.707	0.89
29_M	41_E	0.704	0.88
55_P	58_K	0.699	0.88
8_G	18_L	0.680	0.87
53_V	71_L	0.672	0.86
29_M	38_D	0.666	0.85
64_P	68_V	0.663	0.85
28_E	36_T	0.659	0.85
21_A	49_W	0.656	0.85
5_K	16_T	0.656	0.85
16_T	19_K	0.650	0.84
26_T	29_M	0.637	0.83
7_N	16_T	0.637	0.83
48_E	61_E	0.623	0.81
3_L	6_E	0.614	0.81
49_W	66_L	0.612	0.80
52_S	62_K	0.608	0.80
11_E	14_Y	0.607	0.80
35_D	43_K	0.605	0.80
47_R	57_E	0.605	0.80
20_Y	42_D	0.594	0.78
25_I	35_D	0.591	0.78
53_V	62_K	0.581	0.77
23_V	32_S	0.580	0.77
56_P	59_K	0.577	0.76
32_S	37_L	0.576	0.76
1_S	7_N	0.568	0.75
23_V	37_L	0.564	0.75
58_K	62_K	0.563	0.75
7_N	51_E	0.563	0.75
44_E	52_S	0.563	0.75
37_L	65_L	0.561	0.74
70_N	73_F	0.548	0.73
25_I	39_L	0.547	0.72
22_G	45_K	0.546	0.72
24_D	27_P	0.536	0.71
61_E	65_L	0.535	0.71
26_T	59_K	0.532	0.70
5_K	72_S	0.531	0.70
41_E	73_F	0.530	0.70
52_S	55_P	0.530	0.70
1_S	4_L	0.529	0.70
1_S	19_K	0.525	0.69
7_N	19_K	0.516	0.68
64_P	69_E	0.513	0.68
17_A	37_L	0.507	0.67
25_I	71_L	0.506	0.67
25_I	49_W	0.505	0.66
11_E	50_F	0.500	0.66

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
2dajA	1	0.3562	16.7	0.873	Contact Map
4yycA	2	0.8767	12.9	0.88	Contact Map
3iecE	1	0.0822	11.9	0.881	Contact Map
2qneA	2	0.8767	11	0.883	Contact Map
2zu0C	1	0.1233	8.5	0.889	Contact Map
2w4lA	3	0.589	6.8	0.894	Contact Map
3cmuA	1	0.8904	6.7	0.894	Contact Map
3kkaC	1	0.7671	6.5	0.894	Contact Map
3h8mA	1	0.7808	6	0.896	Contact Map
1a9xA	3	0.9589	5.8	0.897	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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