YABK - BACSU - GREMLIN Contacts

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YABK - Uncharacterized protein YabK

UniProt:	P37553	Sequences: MALHYYCRHCGVKVGSLESSMVSTDSLGFQHLTNEERNDMISYKENGDVHVLTICEDCQEALDRNPHYHEYHTFIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	76 (76)
Sequences:	152 (117)
Seq/√Len:	13.4

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_V	53_T	3.666	0.99
59_Q	63_D	3.098	0.97
29_F	41_I	2.744	0.95
29_F	51_V	2.570	0.93
44_K	48_D	2.357	0.89
25_D	30_Q	2.301	0.88
56_E	59_Q	2.180	0.85
4_H	16_S	2.144	0.84
17_L	22_V	2.088	0.82
24_T	75_I	2.082	0.82
57_D	75_I	1.932	0.76
2_A	16_S	1.791	0.71
41_I	45_E	1.769	0.70
67_H	70_E	1.730	0.68
30_Q	34_N	1.729	0.68
2_A	11_G	1.590	0.61
39_D	63_D	1.469	0.55
53_T	59_Q	1.461	0.54
39_D	52_L	1.318	0.47
26_S	49_V	1.240	0.43
3_L	50_H	1.194	0.40
71_Y	76_Q	1.167	0.39
38_N	71_Y	1.164	0.39
17_L	30_Q	1.155	0.38
33_T	76_Q	1.142	0.38
18_E	21_M	1.140	0.38
12_V	22_V	1.117	0.36
27_L	47_G	1.069	0.34
14_V	35_E	1.065	0.34
12_V	52_L	1.062	0.34
31_H	57_D	1.052	0.33
20_S	45_E	1.043	0.33
6_Y	68_Y	1.038	0.33
40_M	54_I	1.001	0.31
42_S	48_D	1.000	0.31
54_I	72_H	0.990	0.30
68_Y	74_F	0.978	0.30
6_Y	52_L	0.971	0.30
37_R	59_Q	0.962	0.29
61_A	68_Y	0.959	0.29
68_Y	73_T	0.948	0.29
13_K	20_S	0.939	0.28
60_E	64_R	0.938	0.28
73_T	76_Q	0.923	0.28
57_D	60_E	0.903	0.27
61_A	73_T	0.903	0.27
33_T	36_E	0.888	0.26
51_V	73_T	0.886	0.26
59_Q	69_H	0.885	0.26
12_V	17_L	0.884	0.26
24_T	37_R	0.879	0.26
11_G	14_V	0.877	0.26
26_S	35_E	0.873	0.25
30_Q	36_E	0.866	0.25
48_D	60_E	0.854	0.25
62_L	68_Y	0.852	0.25
17_L	53_T	0.851	0.25
18_E	46_N	0.822	0.23
61_A	76_Q	0.817	0.23
34_N	40_M	0.817	0.23
24_T	70_E	0.810	0.23
31_H	51_V	0.805	0.23
53_T	65_N	0.803	0.23
4_H	20_S	0.800	0.23
11_G	21_M	0.778	0.22
34_N	63_D	0.758	0.21
3_L	22_V	0.749	0.21
3_L	30_Q	0.738	0.20
34_N	50_H	0.724	0.20
18_E	26_S	0.710	0.19
16_S	71_Y	0.709	0.19
40_M	70_E	0.699	0.19
39_D	51_V	0.683	0.19
3_L	25_D	0.676	0.18
18_E	24_T	0.675	0.18
31_H	70_E	0.662	0.18
16_S	29_F	0.660	0.18
41_I	51_V	0.651	0.18
39_D	43_Y	0.644	0.17
6_Y	34_N	0.641	0.17
27_L	51_V	0.640	0.17
49_V	64_R	0.623	0.17
15_G	63_D	0.623	0.17
39_D	64_R	0.619	0.17
23_S	53_T	0.619	0.17
13_K	16_S	0.617	0.17
57_D	64_R	0.616	0.17
46_N	62_L	0.611	0.16
29_F	73_T	0.607	0.16
38_N	48_D	0.604	0.16
12_V	35_E	0.602	0.16
61_A	65_N	0.595	0.16
18_E	31_H	0.592	0.16
8_R	22_V	0.592	0.16
53_T	74_F	0.589	0.16
20_S	67_H	0.587	0.16
16_S	52_L	0.585	0.16
31_H	73_T	0.577	0.15
43_Y	49_V	0.576	0.15
54_I	69_H	0.575	0.15
34_N	42_S	0.560	0.15
64_R	67_H	0.558	0.15
69_H	72_H	0.556	0.15
31_H	75_I	0.556	0.15
3_L	73_T	0.554	0.15
43_Y	50_H	0.547	0.15
46_N	49_V	0.546	0.15
16_S	20_S	0.518	0.14
45_E	49_V	0.514	0.14
23_S	42_S	0.514	0.14
59_Q	64_R	0.509	0.14
9_H	43_Y	0.504	0.13
3_L	36_E	0.504	0.13
14_V	26_S	0.500	0.13

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
1vq0A	2	0.7632	80.9	0.875	Contact Map
1vzyA	3	0.7763	77.1	0.88	Contact Map
1i7fA	2	0.1053	73.8	0.883	Contact Map
2xigA	4	0.6447	43.1	0.903	Contact Map
1twfI	1	0.3421	39.3	0.906	Contact Map
2fe3A	2	0.6579	34.7	0.908	Contact Map
2o03A	2	0.5921	34.4	0.908	Contact Map
3eyyA	2	0.5658	33.6	0.909	Contact Map
1zvfA	2	0.7368	33.6	0.909	Contact Map
3ja82	1	0.6711	32.6	0.91	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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