YHJD - BACSU - GREMLIN Contacts

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YHJD - Uncharacterized protein YhjD

UniProt:	O07558	Sequences: MPNLQEEIYDLIERALFLPMAITIFNRDLAGIEESTLKLKHPYKQLISESLKIAQKDLMEVRKELRKRKIAIRETERDEAFTLYTFVIDGYEENHRYFNPRIREQVSELLTYYLFAPDRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	120 (116)
Sequences:	103 (85)
Seq/√Len:	7.9

BACSU - YHJD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_L	44_K	3.060	0.88
74_E	77_R	2.986	0.87
19_P	113_Y	2.937	0.86
102_I	107_S	2.527	0.76
22_I	51_L	2.474	0.74
20_M	103_R	2.306	0.68
93_E	98_F	2.259	0.67
60_E	67_K	2.095	0.61
83_L	96_R	1.965	0.56
42_P	46_L	1.919	0.54
32_I	79_E	1.915	0.53
86_F	103_R	1.837	0.50
2_P	96_R	1.816	0.49
102_I	106_V	1.796	0.49
40_K	97_Y	1.656	0.43
65_L	69_K	1.620	0.42
44_K	76_E	1.592	0.40
71_A	110_L	1.584	0.40
27_R	31_G	1.565	0.39
63_K	87_V	1.496	0.37
4_L	37_L	1.486	0.36
30_A	56_K	1.434	0.34
16_L	39_L	1.432	0.34
32_I	47_I	1.412	0.34
25_F	47_I	1.382	0.33
66_R	82_T	1.373	0.32
16_L	62_R	1.366	0.32
93_E	100_P	1.350	0.31
14_R	62_R	1.327	0.31
65_L	79_E	1.290	0.29
107_S	111_T	1.271	0.29
40_K	44_K	1.253	0.28
101_R	113_Y	1.251	0.28
20_M	86_F	1.240	0.28
56_K	60_E	1.229	0.27
83_L	94_N	1.229	0.27
16_L	104_E	1.220	0.27
41_H	50_S	1.208	0.27
48_S	62_R	1.204	0.27
100_P	103_R	1.192	0.26
17_F	104_E	1.191	0.26
12_I	84_Y	1.187	0.26
70_I	107_S	1.182	0.26
5_Q	110_L	1.144	0.25
12_I	65_L	1.144	0.25
2_P	85_T	1.140	0.25
75_T	87_V	1.139	0.25
59_M	73_R	1.139	0.25
51_L	54_A	1.124	0.24
102_I	111_T	1.121	0.24
65_L	115_F	1.107	0.24
50_S	114_L	1.107	0.24
6_E	76_E	1.106	0.24
65_L	70_I	1.103	0.23
31_G	54_A	1.103	0.23
13_E	101_R	1.096	0.23
65_L	111_T	1.074	0.23
84_Y	116_A	1.065	0.22
61_V	89_D	1.051	0.22
9_Y	48_S	1.044	0.22
21_A	112_Y	1.043	0.22
23_T	27_R	1.027	0.21
22_I	54_A	1.019	0.21
57_D	70_I	1.019	0.21
12_I	70_I	1.012	0.21
82_T	99_N	1.006	0.21
40_K	110_L	0.999	0.21
81_F	93_E	0.998	0.21
50_S	54_A	0.992	0.20
15_A	55_Q	0.990	0.20
29_L	35_S	0.979	0.20
21_A	41_H	0.978	0.20
42_P	64_E	0.978	0.20
59_M	69_K	0.970	0.20
20_M	97_Y	0.963	0.20
44_K	72_I	0.952	0.19
14_R	103_R	0.940	0.19
27_R	35_S	0.919	0.19
11_L	48_S	0.919	0.19
57_D	113_Y	0.915	0.18
1_M	81_F	0.914	0.18
79_E	86_F	0.914	0.18
39_L	46_L	0.890	0.18
74_E	84_Y	0.886	0.18
64_E	69_K	0.884	0.18
80_A	111_T	0.881	0.18
64_E	68_R	0.854	0.17
10_D	56_K	0.843	0.17
66_R	89_D	0.841	0.17
56_K	91_Y	0.841	0.17
57_D	65_L	0.837	0.17
41_H	102_I	0.828	0.16
39_L	78_D	0.826	0.16
36_T	44_K	0.817	0.16
68_R	73_R	0.817	0.16
4_L	50_S	0.807	0.16
32_I	40_K	0.807	0.16
5_Q	104_E	0.806	0.16
8_I	89_D	0.805	0.16
14_R	61_V	0.804	0.16
19_P	57_D	0.801	0.16
45_Q	57_D	0.800	0.16
22_I	83_L	0.795	0.16
36_T	63_K	0.794	0.16
25_F	70_I	0.791	0.16
8_I	95_H	0.790	0.16
32_I	70_I	0.790	0.16
70_I	85_T	0.786	0.15
25_F	51_L	0.781	0.15
54_A	106_V	0.780	0.15
86_F	97_Y	0.779	0.15
24_I	34_E	0.778	0.15
15_A	19_P	0.777	0.15
96_R	105_Q	0.762	0.15
25_F	114_L	0.750	0.15
13_E	97_Y	0.742	0.15
56_K	67_K	0.715	0.14
17_F	113_Y	0.714	0.14
11_L	68_R	0.712	0.14
30_A	62_R	0.708	0.14
52_K	55_Q	0.705	0.14
24_I	89_D	0.704	0.14
7_E	63_K	0.698	0.14
77_R	111_T	0.694	0.14
80_A	102_I	0.690	0.14
19_P	101_R	0.689	0.14
38_K	103_R	0.678	0.13
55_Q	91_Y	0.673	0.13
81_F	99_N	0.672	0.13
30_A	66_R	0.665	0.13
14_R	24_I	0.664	0.13
41_H	94_N	0.652	0.13
17_F	54_A	0.649	0.13
24_I	27_R	0.647	0.13
26_N	51_L	0.644	0.13
24_I	69_K	0.637	0.13
18_L	27_R	0.634	0.13
47_I	57_D	0.633	0.12
32_I	35_S	0.630	0.12
15_A	62_R	0.630	0.12
45_Q	67_K	0.623	0.12
84_Y	102_I	0.610	0.12
46_L	57_D	0.602	0.12
51_L	91_Y	0.593	0.12
27_R	55_Q	0.593	0.12
84_Y	96_R	0.588	0.12
32_I	42_P	0.588	0.12
69_K	91_Y	0.582	0.12
77_R	102_I	0.578	0.12
43_Y	46_L	0.577	0.12
10_D	82_T	0.573	0.11
80_A	83_L	0.571	0.11
47_I	114_L	0.570	0.11
29_L	116_A	0.570	0.11
7_E	69_K	0.564	0.11
54_A	66_R	0.556	0.11
9_Y	72_I	0.555	0.11
71_A	78_D	0.554	0.11
54_A	61_V	0.554	0.11
112_Y	116_A	0.551	0.11
13_E	109_L	0.551	0.11
8_I	50_S	0.545	0.11
74_E	102_I	0.540	0.11
33_E	56_K	0.540	0.11
92_E	106_V	0.536	0.11
15_A	25_F	0.536	0.11
25_F	49_E	0.535	0.11
6_E	11_L	0.532	0.11
6_E	65_L	0.523	0.11
70_I	74_E	0.511	0.10
3_N	96_R	0.510	0.10
85_T	116_A	0.509	0.10
100_P	106_V	0.503	0.10
44_K	84_Y	0.500	0.10

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
4bouA	2	0.4917	6.1	0.95	Contact Map
4d7sA	3	0.6083	6.1	0.95	Contact Map
3uknA	2	0.5917	5.3	0.951	Contact Map
4ltoA	3	0.5417	4.9	0.952	Contact Map
3vn0A	2	0.3583	4.9	0.952	Contact Map
1pp9F	1	0.5	4.7	0.952	Contact Map
2ptmA	3	0.6083	4.1	0.954	Contact Map
1mw9X	1	0.5917	3.7	0.955	Contact Map
1th5A	1	0.5417	3.6	0.955	Contact Map
4cbcA	3	0.2417	3.4	0.955	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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