YHZD - BACSU - GREMLIN Contacts

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YHZD - Uncharacterized protein YhzD

UniProt:	C0H3Y1	Sequences: MADYFLTVFDPSGNTLVNEQFEAEHEEAAKTHGEALLKEKELHSHTHRLVNAAGKLILFHR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	61 (60)
Sequences:	108 (90)
Seq/√Len:	11.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_V	42_L	5.174	1.00
21_F	49_L	2.679	0.91
36_L	40_K	2.671	0.91
24_E	28_A	2.026	0.74
10_D	45_H	2.013	0.74
34_E	38_K	1.941	0.71
23_A	37_L	1.753	0.63
31_T	34_E	1.684	0.60
26_E	52_A	1.629	0.57
10_D	16_L	1.627	0.57
15_T	18_N	1.578	0.55
6_L	23_A	1.525	0.52
6_L	49_L	1.473	0.49
21_F	37_L	1.397	0.46
8_V	45_H	1.354	0.44
22_E	25_H	1.353	0.43
38_K	43_H	1.328	0.42
6_L	37_L	1.290	0.40
11_P	27_E	1.270	0.39
32_H	35_A	1.217	0.37
34_E	43_H	1.164	0.35
8_V	16_L	1.154	0.34
3_D	22_E	1.121	0.33
22_E	34_E	1.081	0.31
11_P	20_Q	1.074	0.31
15_T	50_V	1.050	0.30
49_L	57_I	1.042	0.29
5_F	18_N	1.041	0.29
36_L	51_N	1.018	0.28
44_S	60_H	1.005	0.28
11_P	39_E	0.981	0.27
26_E	60_H	0.977	0.27
40_K	54_G	0.956	0.26
32_H	36_L	0.943	0.25
2_A	26_E	0.940	0.25
2_A	54_G	0.901	0.24
14_N	30_K	0.889	0.23
32_H	42_L	0.884	0.23
26_E	41_E	0.846	0.22
26_E	57_I	0.843	0.22
19_E	36_L	0.841	0.22
51_N	57_I	0.835	0.22
41_E	53_A	0.831	0.21
24_E	31_T	0.823	0.21
6_L	21_F	0.801	0.20
9_F	49_L	0.798	0.20
6_L	58_L	0.794	0.20
17_V	28_A	0.787	0.20
15_T	49_L	0.786	0.20
5_F	36_L	0.779	0.20
36_L	42_L	0.771	0.20
4_Y	18_N	0.769	0.19
9_F	47_H	0.765	0.19
15_T	51_N	0.765	0.19
50_V	53_A	0.746	0.19
10_D	18_N	0.739	0.19
29_A	58_L	0.737	0.19
25_H	50_V	0.711	0.18
17_V	49_L	0.707	0.18
2_A	53_A	0.704	0.18
18_N	56_L	0.695	0.17
51_N	55_K	0.695	0.17
5_F	40_K	0.689	0.17
20_Q	45_H	0.685	0.17
2_A	22_E	0.682	0.17
41_E	44_S	0.678	0.17
12_S	43_H	0.674	0.17
16_L	36_L	0.669	0.17
45_H	54_G	0.645	0.16
52_A	60_H	0.642	0.16
26_E	45_H	0.633	0.16
10_D	40_K	0.617	0.15
9_F	15_T	0.606	0.15
23_A	51_N	0.600	0.15
14_N	45_H	0.570	0.14
5_F	52_A	0.556	0.14
42_L	55_K	0.542	0.13
41_E	60_H	0.540	0.13
22_E	27_E	0.540	0.13
51_N	56_L	0.532	0.13
3_D	16_L	0.531	0.13
29_A	47_H	0.526	0.13
2_A	27_E	0.516	0.13
31_T	45_H	0.516	0.13
31_T	35_A	0.514	0.13
11_P	18_N	0.514	0.13
18_N	26_E	0.506	0.13
14_N	38_K	0.506	0.13
26_E	43_H	0.505	0.13
20_Q	25_H	0.500	0.12

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
2oycA	2	1	28.4	0.893	Contact Map
2j3tC	1	0.9672	27.3	0.894	Contact Map
2zosA	1	0.9016	22.7	0.897	Contact Map
1qksA	2	0.9836	15.8	0.904	Contact Map
3cueC	1	0.9508	13.7	0.908	Contact Map
1nirA	2	0.918	13.6	0.908	Contact Map
2dhoA	1	0.7377	11.4	0.911	Contact Map
4nkpA	5	0.7377	10.8	0.911	Contact Map
4hvtA	1	1	9.1	0.915	Contact Map
2x4dA	2	1	9	0.915	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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