YPJD - BACSU - GREMLIN Contacts

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YPJD - Uncharacterized protein YpjD

UniProt:	P42979	Sequences: MSDKTMKDIQAEVDRYIGQFKEGYFSPLAMMARLTEELGELAREVNHRYGEKPKKATEDDKSMEEEIGDVLFVLVCLANSLDISLEEAHDRVMHKFNTRDKDRWTRKEEGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	111 (103)
Sequences:	547 (196)
Seq/√Len:	19.3

BACSU - YPJD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_E	92_V	3.970	1.00
26_S	51_E	3.480	1.00
12_E	97_N	3.204	0.99
89_H	93_M	2.905	0.99
11_A	15_R	2.665	0.98
41_L	67_I	2.601	0.98
31_M	35_T	2.518	0.97
7_K	84_S	2.421	0.96
9_I	75_V	2.338	0.96
67_I	74_L	2.338	0.96
16_Y	21_K	2.263	0.95
64_E	88_A	2.260	0.95
67_I	77_L	2.190	0.94
9_I	89_H	2.075	0.92
22_E	105_T	2.053	0.91
45_V	77_L	1.851	0.86
12_E	90_D	1.783	0.84
68_G	92_V	1.762	0.83
28_L	32_A	1.749	0.83
75_V	85_L	1.731	0.82
38_L	70_V	1.560	0.75
98_T	101_K	1.559	0.74
31_M	72_F	1.515	0.72
22_E	104_W	1.501	0.72
94_H	98_T	1.481	0.71
87_E	91_R	1.469	0.70
86_E	90_D	1.438	0.68
35_T	72_F	1.383	0.65
38_L	89_H	1.358	0.64
31_M	38_L	1.350	0.63
56_A	59_D	1.332	0.62
48_R	62_S	1.297	0.60
5_T	91_R	1.261	0.58
7_K	11_A	1.256	0.57
61_K	65_E	1.246	0.57
20_F	72_F	1.239	0.56
12_E	94_H	1.239	0.56
31_M	42_A	1.230	0.56
34_L	77_L	1.186	0.53
72_F	93_M	1.109	0.48
29_A	53_P	1.089	0.47
53_P	104_W	1.049	0.44
9_I	93_M	1.042	0.44
22_E	53_P	1.032	0.43
98_T	102_D	1.008	0.42
20_F	31_M	1.008	0.42
11_A	75_V	0.995	0.41
28_L	46_N	0.991	0.41
16_Y	30_M	0.977	0.40
92_V	96_F	0.967	0.39
29_A	51_E	0.935	0.37
25_F	73_V	0.930	0.37
53_P	107_K	0.913	0.36
42_A	46_N	0.905	0.36
8_D	12_E	0.892	0.35
30_M	53_P	0.871	0.34
56_A	63_M	0.861	0.33
7_K	94_H	0.851	0.32
90_D	94_H	0.840	0.32
6_M	75_V	0.817	0.31
30_M	76_C	0.812	0.30
15_R	19_Q	0.812	0.30
76_C	104_W	0.810	0.30
20_F	33_R	0.804	0.30
72_F	105_T	0.798	0.30
7_K	90_D	0.789	0.29
51_E	81_L	0.783	0.29
53_P	105_T	0.775	0.28
17_I	88_A	0.771	0.28
20_F	35_T	0.771	0.28
62_S	91_R	0.763	0.28
91_R	94_H	0.759	0.28
5_T	8_D	0.751	0.27
30_M	80_S	0.750	0.27
87_E	90_D	0.749	0.27
64_E	68_G	0.746	0.27
30_M	104_W	0.744	0.27
36_E	40_E	0.740	0.27
41_L	63_M	0.734	0.26
22_E	30_M	0.732	0.26
18_G	105_T	0.728	0.26
30_M	34_L	0.725	0.26
29_A	81_L	0.721	0.26
26_S	29_A	0.716	0.25
45_V	74_L	0.710	0.25
25_F	96_F	0.708	0.25
47_H	52_K	0.706	0.25
19_Q	45_V	0.706	0.25
10_Q	88_A	0.698	0.25
12_E	93_M	0.696	0.24
102_D	106_R	0.689	0.24
11_A	90_D	0.688	0.24
21_K	77_L	0.682	0.24
48_R	60_D	0.669	0.23
56_A	90_D	0.661	0.23
23_G	44_E	0.655	0.23
16_Y	38_L	0.651	0.22
46_N	52_K	0.651	0.22
71_L	86_E	0.651	0.22
32_A	35_T	0.647	0.22
20_F	106_R	0.646	0.22
6_M	9_I	0.638	0.22
41_L	92_V	0.632	0.22
91_R	102_D	0.630	0.22
27_P	54_K	0.630	0.22
89_H	92_V	0.629	0.21
23_G	52_K	0.626	0.21
57_T	61_K	0.624	0.21
6_M	68_G	0.618	0.21
49_Y	81_L	0.616	0.21
5_T	86_E	0.615	0.21
23_G	27_P	0.612	0.21
73_V	96_F	0.610	0.21
43_R	58_E	0.608	0.21
64_E	77_L	0.607	0.21
64_E	92_V	0.596	0.20
31_M	70_V	0.594	0.20
41_L	44_E	0.594	0.20
100_D	103_R	0.592	0.20
7_K	35_T	0.592	0.20
15_R	94_H	0.589	0.20
13_V	88_A	0.588	0.20
75_V	89_H	0.586	0.20
31_M	45_V	0.577	0.19
59_D	65_E	0.576	0.19
25_F	51_E	0.575	0.19
44_E	48_R	0.572	0.19
86_E	92_V	0.570	0.19
21_K	107_K	0.568	0.19
12_E	89_H	0.567	0.19
44_E	52_K	0.559	0.19
71_L	102_D	0.558	0.19
75_V	98_T	0.558	0.19
62_S	65_E	0.556	0.19
65_E	68_G	0.552	0.18
8_D	11_A	0.546	0.18
33_R	47_H	0.541	0.18
18_G	22_E	0.538	0.18
34_L	73_V	0.537	0.18
17_I	51_E	0.529	0.17
20_F	105_T	0.527	0.17
47_H	80_S	0.524	0.17
86_E	91_R	0.523	0.17
60_D	83_I	0.522	0.17
56_A	60_D	0.512	0.17
49_Y	73_V	0.512	0.17
41_L	68_G	0.506	0.17
43_R	50_G	0.506	0.17
72_F	83_I	0.506	0.17
11_A	84_S	0.506	0.17
29_A	48_R	0.504	0.17
48_R	71_L	0.503	0.17
33_R	72_F	0.502	0.17
15_R	87_E	0.500	0.16

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
2gtaA	4	0.9459	99.9	0.566	Contact Map
4dk2A	2	0.8198	99.7	0.649	Contact Map
2q73A	4	0.8198	99.7	0.666	Contact Map
2q5zA	4	0.8559	99.6	0.682	Contact Map
2a3qA	3	0.9369	99.6	0.686	Contact Map
4qgpA	4	0.9189	99.6	0.686	Contact Map
2yf4A	5	0.9369	99.5	0.694	Contact Map
2oieA	3	0.8559	99.5	0.696	Contact Map
1vmgA	4	0.6847	99.2	0.738	Contact Map
3craA	2	0.8559	99.2	0.746	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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