YBZG - BACSU - GREMLIN Contacts

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YBZG - Putative ribosome-binding protein YbzG

UniProt:	C0H3S8	Sequences: MIGQKAWVNIGKTEFILLLVVGILTIINVLTADGEKRTFHSPKKKNINHLTLYDCVSPEVQNSINETGRVTNFF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	74 (71)
Sequences:	147 (112)
Seq/√Len:	13.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_K	38_T	2.625	0.93
41_S	67_T	2.588	0.93
7_W	51_T	2.436	0.90
13_T	35_E	2.435	0.90
14_E	38_T	2.325	0.88
39_F	57_S	2.312	0.88
31_T	50_L	2.159	0.84
2_I	64_I	2.081	0.81
46_N	70_V	1.981	0.78
20_V	47_I	1.947	0.77
20_V	52_L	1.760	0.69
24_L	30_L	1.700	0.66
21_V	40_H	1.559	0.59
13_T	50_L	1.548	0.58
63_S	67_T	1.500	0.56
23_I	50_L	1.475	0.55
62_N	65_N	1.458	0.54
66_E	71_T	1.432	0.52
57_S	60_V	1.427	0.52
29_V	54_D	1.426	0.52
8_V	18_L	1.421	0.52
30_L	53_Y	1.335	0.47
8_V	16_I	1.269	0.44
8_V	36_K	1.188	0.40
31_T	54_D	1.136	0.37
27_I	68_G	1.136	0.37
18_L	31_T	1.102	0.35
18_L	69_R	1.098	0.35
15_F	54_D	1.083	0.34
36_K	60_V	1.070	0.34
59_E	63_S	1.055	0.33
17_L	44_K	1.054	0.33
13_T	31_T	1.048	0.33
32_A	71_T	1.044	0.33
61_Q	64_I	1.042	0.33
60_V	71_T	1.028	0.32
5_K	55_C	1.007	0.31
14_E	61_Q	0.993	0.30
5_K	53_Y	0.992	0.30
4_Q	36_K	0.988	0.30
2_I	55_C	0.959	0.29
8_V	41_S	0.946	0.28
44_K	51_T	0.945	0.28
21_V	32_A	0.944	0.28
38_T	47_I	0.908	0.27
18_L	46_N	0.883	0.26
19_L	68_G	0.867	0.25
19_L	44_K	0.858	0.25
47_I	52_L	0.847	0.24
18_L	44_K	0.835	0.24
40_H	69_R	0.823	0.23
38_T	61_Q	0.814	0.23
58_P	62_N	0.812	0.23
9_N	28_N	0.810	0.23
22_G	42_P	0.808	0.23
61_Q	65_N	0.804	0.23
10_I	42_P	0.804	0.23
2_I	65_N	0.790	0.22
7_W	57_S	0.788	0.22
5_K	28_N	0.787	0.22
51_T	69_R	0.784	0.22
30_L	42_P	0.772	0.21
22_G	55_C	0.765	0.21
63_S	71_T	0.736	0.20
4_Q	56_V	0.734	0.20
4_Q	52_L	0.734	0.20
32_A	69_R	0.730	0.20
24_L	62_N	0.723	0.20
28_N	51_T	0.721	0.20
60_V	63_S	0.718	0.20
29_V	50_L	0.711	0.19
6_A	56_V	0.710	0.19
23_I	47_I	0.686	0.19
22_G	30_L	0.681	0.18
31_T	38_T	0.680	0.18
29_V	35_E	0.672	0.18
35_E	65_N	0.665	0.18
52_L	71_T	0.652	0.17
9_N	26_I	0.644	0.17
63_S	68_G	0.640	0.17
23_I	64_I	0.638	0.17
46_N	67_T	0.630	0.17
24_L	47_I	0.623	0.17
57_S	63_S	0.619	0.16
63_S	66_E	0.614	0.16
23_I	51_T	0.601	0.16
40_H	63_S	0.591	0.16
2_I	24_L	0.580	0.15
20_V	25_T	0.577	0.15
28_N	46_N	0.568	0.15
28_N	31_T	0.568	0.15
10_I	20_V	0.563	0.15
16_I	20_V	0.558	0.15
52_L	66_E	0.557	0.15
26_I	67_T	0.557	0.15
17_L	53_Y	0.550	0.15
18_L	42_P	0.539	0.14
6_A	47_I	0.525	0.14
15_F	58_P	0.522	0.14
31_T	69_R	0.521	0.14
6_A	20_V	0.520	0.14
7_W	53_Y	0.511	0.14
55_C	64_I	0.508	0.14
52_L	57_S	0.506	0.13
12_K	64_I	0.503	0.13
9_N	58_P	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
4w20M	1	0.973	99.4	0.58	Contact Map
3zf7P	1	0.9595	99.3	0.597	Contact Map
4a18F	1	0.9459	99.2	0.608	Contact Map
3j215	1	0.9595	99.2	0.617	Contact Map
3j61M	1	0.9189	99.2	0.623	Contact Map
4ujqO	1	0.9595	99.1	0.625	Contact Map
3j39M	1	0.9595	99.1	0.625	Contact Map
2joyA	1	0.973	99.1	0.63	Contact Map
1vx7N	1	0.9595	99	0.64	Contact Map
1vx71	1	1	98.7	0.678	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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