YTRH - BACSU - GREMLIN Contacts

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YTRH - Sporulation membrane protein YtrH

UniProt:	C0H3P8	Sequences: MDQEAGFMVNFINSYFIALGVLIGGALIGGLGAYLAGEPPLTAITKLANRLKIWALVAAIGGTFDAVYSFERGILEGNTRDIFKQLLLIISAMGGAQSGWLIISWLTQEHLSS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	113 (103)
Sequences:	175 (122)
Seq/√Len:	12.0

BACSU - YTRH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
15_Y	98_S	3.657	0.99
25_G	51_L	2.651	0.92
65_D	105_W	2.410	0.87
75_L	82_I	2.371	0.86
47_L	51_L	2.252	0.83
93_M	99_G	2.191	0.81
72_R	82_I	2.131	0.79
34_Y	68_Y	1.903	0.71
19_L	97_Q	1.781	0.65
35_L	38_E	1.765	0.65
31_L	66_A	1.751	0.64
49_N	99_G	1.698	0.62
8_M	52_K	1.693	0.61
51_L	83_F	1.691	0.61
16_F	92_A	1.655	0.60
21_V	96_A	1.610	0.57
6_G	99_G	1.598	0.57
29_G	47_L	1.552	0.54
21_V	37_G	1.548	0.54
51_L	57_V	1.538	0.54
105_W	108_Q	1.529	0.53
67_V	75_L	1.519	0.53
17_I	21_V	1.518	0.53
89_I	97_Q	1.516	0.53
9_V	82_I	1.505	0.52
18_A	39_P	1.474	0.51
12_I	36_A	1.448	0.49
11_F	87_L	1.428	0.48
63_T	84_K	1.425	0.48
77_G	96_A	1.425	0.48
42_T	46_K	1.414	0.48
23_I	102_I	1.398	0.47
29_G	105_W	1.369	0.45
6_G	9_V	1.338	0.44
11_F	91_S	1.331	0.43
26_A	48_A	1.309	0.42
7_F	23_I	1.283	0.41
15_Y	107_T	1.283	0.41
32_G	56_L	1.271	0.40
55_A	58_A	1.266	0.40
63_T	89_I	1.234	0.39
70_F	93_M	1.211	0.38
12_I	58_A	1.210	0.38
52_K	96_A	1.200	0.37
46_K	98_S	1.200	0.37
83_F	87_L	1.191	0.37
23_I	76_E	1.178	0.36
29_G	108_Q	1.165	0.35
26_A	76_E	1.149	0.35
51_L	65_D	1.141	0.34
98_S	106_L	1.133	0.34
87_L	103_I	1.128	0.34
72_R	81_D	1.113	0.33
18_A	35_L	1.086	0.32
74_I	81_D	1.077	0.32
32_G	51_L	1.071	0.31
37_G	64_F	1.069	0.31
46_K	63_T	1.046	0.30
9_V	104_S	1.010	0.29
33_A	52_K	1.010	0.29
39_P	76_E	1.009	0.29
29_G	84_K	1.008	0.29
8_M	80_R	1.004	0.28
32_G	99_G	1.000	0.28
64_F	73_G	0.993	0.28
50_R	74_I	0.963	0.27
7_F	19_L	0.963	0.27
49_N	90_I	0.941	0.26
82_I	86_L	0.927	0.25
32_G	48_A	0.910	0.25
14_S	30_G	0.906	0.25
34_Y	63_T	0.904	0.25
38_E	84_K	0.896	0.24
41_L	45_T	0.838	0.22
31_L	38_E	0.829	0.22
75_L	97_Q	0.813	0.21
92_A	98_S	0.804	0.21
58_A	66_A	0.804	0.21
6_G	38_E	0.797	0.21
71_E	77_G	0.793	0.21
35_L	74_I	0.780	0.20
21_V	58_A	0.772	0.20
16_F	23_I	0.751	0.19
21_V	77_G	0.748	0.19
28_I	102_I	0.743	0.19
80_R	100_W	0.737	0.19
30_G	96_A	0.737	0.19
30_G	44_I	0.734	0.19
21_V	103_I	0.732	0.19
25_G	65_D	0.723	0.18
9_V	91_S	0.715	0.18
68_Y	74_I	0.713	0.18
53_I	65_D	0.709	0.18
27_L	40_P	0.708	0.18
28_I	90_I	0.706	0.18
33_A	38_E	0.693	0.18
46_K	52_K	0.692	0.18
10_N	48_A	0.689	0.17
18_A	57_V	0.688	0.17
30_G	33_A	0.683	0.17
51_L	58_A	0.678	0.17
21_V	55_A	0.664	0.17
53_I	105_W	0.660	0.17
10_N	60_I	0.659	0.17
14_S	67_V	0.659	0.17
48_A	85_Q	0.648	0.16
34_Y	69_S	0.646	0.16
52_K	100_W	0.645	0.16
49_N	76_E	0.644	0.16
74_I	103_I	0.643	0.16
53_I	89_I	0.643	0.16
35_L	57_V	0.642	0.16
30_G	100_W	0.637	0.16
34_Y	107_T	0.627	0.16
6_G	33_A	0.619	0.16
60_I	91_S	0.618	0.15
79_T	93_M	0.610	0.15
73_G	84_K	0.602	0.15
8_M	86_L	0.601	0.15
46_K	75_L	0.598	0.15
7_F	88_L	0.595	0.15
84_K	89_I	0.591	0.15
26_A	97_Q	0.589	0.15
19_L	106_L	0.578	0.14
47_L	67_V	0.578	0.14
66_A	86_L	0.578	0.14
6_G	10_N	0.578	0.14
15_Y	22_L	0.575	0.14
40_P	43_A	0.573	0.14
57_V	67_V	0.572	0.14
41_L	64_F	0.568	0.14
31_L	74_I	0.568	0.14
39_P	56_L	0.565	0.14
34_Y	105_W	0.562	0.14
47_L	91_S	0.559	0.14
22_L	86_L	0.557	0.14
44_I	52_K	0.549	0.14
6_G	78_N	0.544	0.14
35_L	39_P	0.540	0.14
10_N	78_N	0.534	0.13
15_Y	81_D	0.534	0.13
37_G	94_G	0.533	0.13
17_I	79_T	0.531	0.13
7_F	18_A	0.521	0.13
11_F	19_L	0.520	0.13
32_G	82_I	0.518	0.13
9_V	23_I	0.518	0.13
35_L	52_K	0.517	0.13
60_I	81_D	0.517	0.13
18_A	58_A	0.511	0.13
19_L	28_I	0.507	0.13
51_L	84_K	0.504	0.13
36_A	56_L	0.501	0.13
67_V	104_S	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
3llqA	3	0.8673	25.4	0.934	Contact Map
1ldfA	3	0.8142	24.9	0.934	Contact Map
2f2bA	4	0.8584	16.9	0.939	Contact Map
3c02A	3	0.9204	15.1	0.94	Contact Map
1j4nA	4	0.885	14.3	0.941	Contact Map
3zojA	3	0.885	11.5	0.944	Contact Map
3d9sA	3	0.8319	10.2	0.945	Contact Map
2o9gA	3	0.8673	9.7	0.945	Contact Map
4nefA	4	0.8938	8.3	0.947	Contact Map
2b6oA	6	0.8938	7	0.949	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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