YPZJ - BACSU - GREMLIN Contacts

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YPZJ - Uncharacterized protein YpzJ

UniProt:	C0H447	Sequences: MNNKGCIKCGSTEAGQKEIATTGTGLSKLFDVQHNRFLVVYCKNCGYSEFYNKESSTAGNILDLFFGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	68 (65)
Sequences:	176 (107)
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
20_A	24_T	3.596	0.99
39_V	48_S	2.492	0.91
20_A	25_G	2.298	0.87
17_K	35_N	2.293	0.87
55_S	60_N	2.085	0.81
10_G	13_E	1.668	0.64
56_S	60_N	1.652	0.64
19_I	50_F	1.646	0.63
36_R	64_L	1.575	0.60
15_G	43_K	1.535	0.58
15_G	52_N	1.518	0.57
21_T	50_F	1.517	0.57
11_S	62_L	1.478	0.55
7_I	41_Y	1.424	0.52
24_T	35_N	1.420	0.52
41_Y	44_N	1.406	0.51
5_G	65_F	1.287	0.45
4_K	48_S	1.280	0.44
7_I	56_S	1.253	0.43
10_G	61_I	1.251	0.43
16_Q	40_V	1.148	0.38
44_N	61_I	1.147	0.38
31_D	34_H	1.144	0.37
55_S	64_L	1.135	0.37
32_V	44_N	1.133	0.37
27_S	34_H	1.133	0.37
28_K	33_Q	1.130	0.37
38_L	55_S	1.102	0.35
18_E	27_S	1.093	0.35
16_Q	38_L	1.089	0.35
4_K	39_V	1.076	0.34
17_K	20_A	1.059	0.33
12_T	57_T	1.049	0.33
3_N	46_G	1.035	0.32
4_K	54_E	1.027	0.32
40_V	47_Y	0.997	0.30
16_Q	37_F	0.997	0.30
40_V	59_G	0.994	0.30
10_G	46_G	0.988	0.30
28_K	39_V	0.983	0.30
32_V	62_L	0.977	0.30
3_N	50_F	0.962	0.29
10_G	57_T	0.953	0.29
28_K	31_D	0.946	0.28
17_K	34_H	0.920	0.27
39_V	50_F	0.896	0.26
25_G	59_G	0.877	0.25
22_T	33_Q	0.866	0.25
43_K	54_E	0.861	0.25
46_G	58_A	0.856	0.25
27_S	66_F	0.855	0.25
21_T	52_N	0.844	0.24
14_A	66_F	0.837	0.24
19_I	39_V	0.830	0.24
60_N	65_F	0.826	0.23
7_I	47_Y	0.825	0.23
34_H	53_K	0.819	0.23
15_G	47_Y	0.817	0.23
33_Q	60_N	0.815	0.23
14_A	61_I	0.809	0.23
14_A	35_N	0.795	0.22
32_V	64_L	0.792	0.22
3_N	58_A	0.792	0.22
24_T	51_Y	0.791	0.22
41_Y	46_G	0.765	0.21
29_L	54_E	0.763	0.21
19_I	35_N	0.725	0.20
17_K	52_N	0.718	0.20
54_E	57_T	0.715	0.19
4_K	14_A	0.689	0.19
17_K	41_Y	0.677	0.18
38_L	59_G	0.670	0.18
7_I	52_N	0.664	0.18
36_R	48_S	0.661	0.18
4_K	58_A	0.650	0.17
38_L	62_L	0.650	0.17
18_E	38_L	0.644	0.17
5_G	48_S	0.636	0.17
3_N	38_L	0.636	0.17
13_E	19_I	0.630	0.17
53_K	60_N	0.629	0.17
38_L	41_Y	0.625	0.17
12_T	43_K	0.622	0.17
29_L	66_F	0.617	0.16
19_I	48_S	0.612	0.16
24_T	34_H	0.604	0.16
5_G	51_Y	0.599	0.16
26_L	29_L	0.593	0.16
20_A	29_L	0.588	0.16
5_G	56_S	0.583	0.15
47_Y	65_F	0.576	0.15
5_G	67_G	0.570	0.15
30_F	57_T	0.569	0.15
48_S	65_F	0.560	0.15
4_K	61_I	0.529	0.14
36_R	53_K	0.522	0.14
14_A	52_N	0.515	0.14
36_R	62_L	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
2k4xA	1	0.5882	96.1	0.807	Contact Map
4bpe9	1	0.6618	87	0.857	Contact Map
3po3S	1	0.6471	86.2	0.858	Contact Map
1pqvS	1	0.6471	85.4	0.86	Contact Map
3j3af	1	0.5147	83.5	0.863	Contact Map
4ujpg	1	0.5147	83.4	0.863	Contact Map
4uer9	1	0.5147	82.6	0.864	Contact Map
4cuyf	1	0.5147	82.5	0.865	Contact Map
3zey9	1	0.4853	82.2	0.865	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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