YRZL - BACSU - GREMLIN Contacts

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YRZL - UPF0297 protein YrzL

UniProt:	Q7WY61	Sequences: MSSFDKTMKFNFSDDSAETNVNEVLITVYDALQEKGYNPINQIVGYLLSGDPAYIPRHRDARNLIRKLERDELIEELVKSYLEQHKEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	88 (80)
Sequences:	591 (321)
Seq/√Len:	35.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_T	64_L	3.967	1.00
31_A	59_R	3.008	1.00
53_A	56_P	2.969	1.00
24_V	68_L	2.261	0.99
43_I	78_V	2.204	0.99
47_L	53_A	2.198	0.99
10_F	41_N	2.065	0.99
21_V	73_L	1.931	0.98
48_L	74_I	1.927	0.98
50_G	69_E	1.833	0.97
50_G	75_E	1.831	0.97
34_E	59_R	1.783	0.97
60_D	63_N	1.722	0.96
5_D	47_L	1.659	0.95
21_V	68_L	1.557	0.93
69_E	75_E	1.551	0.93
31_A	58_H	1.531	0.92
13_S	63_N	1.508	0.92
24_V	28_V	1.407	0.89
19_T	23_E	1.400	0.88
80_S	84_Q	1.382	0.88
30_D	59_R	1.364	0.87
68_L	73_L	1.350	0.86
53_A	57_R	1.347	0.86
35_K	56_P	1.342	0.86
69_E	72_E	1.330	0.86
80_S	83_E	1.290	0.84
35_K	69_E	1.265	0.83
21_V	75_E	1.237	0.81
20_N	23_E	1.179	0.78
31_A	61_A	1.140	0.75
48_L	66_R	1.134	0.75
76_E	80_S	1.134	0.75
27_T	30_D	1.092	0.72
11_N	57_R	1.087	0.72
12_F	44_V	1.066	0.70
11_N	19_T	1.037	0.68
14_D	78_V	1.021	0.67
50_G	57_R	1.005	0.66
10_F	82_L	1.005	0.66
44_V	64_L	0.979	0.64
25_L	44_V	0.979	0.64
77_L	80_S	0.961	0.62
37_Y	51_D	0.954	0.62
53_A	63_N	0.943	0.61
40_I	79_K	0.924	0.59
4_F	83_E	0.923	0.59
29_Y	39_P	0.916	0.58
8_M	66_R	0.915	0.58
56_P	71_D	0.910	0.58
24_V	63_N	0.891	0.56
50_G	76_E	0.881	0.55
39_P	58_H	0.876	0.55
59_R	67_K	0.871	0.55
65_I	71_D	0.870	0.55
56_P	74_I	0.856	0.53
13_S	19_T	0.852	0.53
32_L	55_I	0.825	0.51
5_D	8_M	0.818	0.50
21_V	60_D	0.803	0.49
13_S	79_K	0.778	0.47
6_K	14_D	0.773	0.46
21_V	69_E	0.773	0.46
47_L	74_I	0.766	0.45
4_F	67_K	0.762	0.45
25_L	43_I	0.751	0.44
20_N	67_K	0.743	0.44
9_K	48_L	0.740	0.43
6_K	9_K	0.732	0.43
11_N	50_G	0.727	0.42
47_L	78_V	0.724	0.42
4_F	22_N	0.720	0.42
8_M	80_S	0.718	0.41
45_G	61_A	0.714	0.41
21_V	50_G	0.706	0.40
24_V	64_L	0.699	0.40
26_I	57_R	0.695	0.39
18_E	58_H	0.695	0.39
20_N	47_L	0.694	0.39
12_F	20_N	0.692	0.39
5_D	77_L	0.691	0.39
79_K	82_L	0.690	0.39
53_A	71_D	0.676	0.38
27_T	31_A	0.673	0.38
73_L	77_L	0.666	0.37
17_A	83_E	0.665	0.37
25_L	55_I	0.657	0.36
18_E	26_I	0.655	0.36
30_D	33_Q	0.655	0.36
4_F	8_M	0.649	0.36
17_A	79_K	0.632	0.34
31_A	35_K	0.629	0.34
19_T	68_L	0.619	0.33
57_R	83_E	0.607	0.32
8_M	75_E	0.606	0.32
28_V	61_A	0.603	0.32
15_D	19_T	0.602	0.32
48_L	82_L	0.596	0.32
37_Y	41_N	0.585	0.31
53_A	74_I	0.574	0.30
6_K	13_S	0.570	0.30
9_K	40_I	0.568	0.30
9_K	63_N	0.566	0.29
21_V	24_V	0.563	0.29
14_D	25_L	0.556	0.29
44_V	78_V	0.550	0.28
49_S	84_Q	0.543	0.28
35_K	39_P	0.540	0.28
30_D	43_I	0.523	0.26
26_I	30_D	0.522	0.26
35_K	66_R	0.517	0.26
66_R	82_L	0.516	0.26
17_A	21_V	0.515	0.26
73_L	76_E	0.515	0.26
5_D	43_I	0.514	0.26
19_T	27_T	0.514	0.26
76_E	79_K	0.509	0.25
48_L	51_D	0.502	0.25
47_L	70_R	0.500	0.25
23_E	27_T	0.500	0.25

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
3va9A	2	0.7614	85.7	0.882	Contact Map
4r3zC	1	0	49.2	0.91	Contact Map
1ujpA	1	0.6705	33.8	0.918	Contact Map
1wmxA	2	0.5227	18.7	0.928	Contact Map
3ih6A	5	0.9545	16.7	0.929	Contact Map
2nrqA	1	0.9091	15	0.931	Contact Map
4jykA	2	0.7614	14.5	0.931	Contact Map
2y8uA	1	0.5682	13.4	0.932	Contact Map
2ekcA	1	0.6818	12.8	0.933	Contact Map
4lgyA	1	1	12.7	0.933	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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