YPHP - BACSU - GREMLIN Contacts

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YPHP - UPF0403 protein YphP

UniProt:	P54170	Sequences: MSMAYEEYMRQLVVPMRRELTGAGFEELTTAEEVENFMEKAEGTTLVVVNSVCGCAAGLARPAATQAVLQNDKTPDNTVTVFAGQDKEATAKMREYFTGQEPSSPSMALLKGKEVVHFIPRHEIEGHDMEEIMKNLTAAFDAHC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	144 (136)
Sequences:	483 (198)
Seq/√Len:	17.0

BACSU - YPHP YQIW

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_A	140_F	5.161	1.00
35_E	92_K	4.039	1.00
14_V	18_R	3.475	1.00
92_K	95_E	3.201	0.99
42_E	112_G	2.924	0.98
64_A	107_M	2.793	0.98
33_E	36_N	2.718	0.97
71_N	141_D	2.495	0.95
57_A	132_I	2.380	0.94
97_F	110_L	2.295	0.93
46_L	136_L	2.274	0.93
117_H	139_A	2.270	0.93
19_E	65_T	2.247	0.92
23_A	65_T	2.120	0.90
69_L	140_F	1.968	0.86
40_K	77_N	1.846	0.82
135_N	139_A	1.803	0.80
18_R	22_G	1.785	0.79
17_R	27_E	1.693	0.76
91_A	95_E	1.682	0.75
49_V	97_F	1.678	0.75
21_T	27_E	1.643	0.73
109_L	140_F	1.571	0.70
16_M	20_L	1.551	0.69
26_E	33_E	1.548	0.69
117_H	135_N	1.527	0.68
8_Y	15_P	1.503	0.66
29_T	86_D	1.470	0.65
93_M	97_F	1.454	0.64
25_F	78_T	1.397	0.61
85_Q	90_T	1.396	0.60
22_G	65_T	1.347	0.58
38_M	93_M	1.314	0.56
90_T	96_Y	1.304	0.55
8_Y	57_A	1.294	0.55
63_A	128_D	1.288	0.54
13_V	79_V	1.287	0.54
71_N	137_T	1.282	0.54
129_M	133_M	1.255	0.52
35_E	96_Y	1.226	0.50
120_P	126_G	1.221	0.50
127_H	135_N	1.169	0.47
37_F	45_T	1.169	0.47
53_C	104_S	1.157	0.46
110_L	115_V	1.156	0.46
108_A	118_F	1.155	0.46
35_E	39_E	1.139	0.45
45_T	79_V	1.137	0.45
43_G	112_G	1.135	0.45
127_H	131_E	1.135	0.45
17_R	85_Q	1.133	0.45
93_M	118_F	1.130	0.45
70_Q	137_T	1.111	0.44
100_Q	120_P	1.102	0.43
101_E	120_P	1.080	0.42
20_L	48_V	1.080	0.42
9_M	59_L	1.080	0.42
73_K	109_L	1.078	0.42
44_T	144_C	1.062	0.41
116_V	143_H	1.060	0.41
81_V	90_T	1.055	0.40
37_F	118_F	1.045	0.40
107_M	112_G	1.042	0.40
63_A	106_S	1.040	0.40
28_L	79_V	1.036	0.39
96_Y	99_G	1.028	0.39
48_V	107_M	1.027	0.39
99_G	120_P	1.022	0.39
25_F	64_A	1.020	0.38
17_R	63_A	1.017	0.38
66_Q	133_M	1.016	0.38
51_S	55_C	1.015	0.38
133_M	136_L	0.986	0.36
30_T	33_E	0.958	0.35
45_T	77_N	0.953	0.35
46_L	139_A	0.939	0.34
100_Q	115_V	0.938	0.34
35_E	87_K	0.937	0.34
100_Q	118_F	0.904	0.32
60_A	63_A	0.903	0.32
92_K	99_G	0.901	0.32
101_E	129_M	0.895	0.32
23_A	64_A	0.887	0.31
66_Q	70_Q	0.886	0.31
26_E	40_K	0.881	0.31
109_L	144_C	0.878	0.31
48_V	57_A	0.848	0.29
37_F	40_K	0.848	0.29
8_Y	132_I	0.848	0.29
19_E	85_Q	0.844	0.29
38_M	96_Y	0.836	0.29
114_E	143_H	0.836	0.29
130_E	134_K	0.821	0.28
98_T	114_E	0.819	0.28
7_E	10_R	0.818	0.28
8_Y	135_N	0.817	0.28
29_T	33_E	0.816	0.28
83_A	94_R	0.815	0.28
66_Q	129_M	0.809	0.27
109_L	139_A	0.805	0.27
59_L	132_I	0.802	0.27
136_L	143_H	0.802	0.27
16_M	57_A	0.801	0.27
70_Q	134_K	0.794	0.27
48_V	132_I	0.790	0.26
109_L	143_H	0.790	0.26
85_Q	97_F	0.783	0.26
93_M	112_G	0.773	0.26
38_M	112_G	0.762	0.25
40_K	45_T	0.753	0.25
123_E	127_H	0.750	0.25
19_E	58_G	0.740	0.24
67_A	137_T	0.732	0.24
117_H	132_I	0.727	0.24
51_S	121_R	0.725	0.24
55_C	121_R	0.725	0.24
20_L	25_F	0.721	0.23
13_V	29_T	0.719	0.23
54_G	94_R	0.715	0.23
109_L	135_N	0.708	0.23
84_G	104_S	0.700	0.22
53_C	84_G	0.699	0.22
47_V	93_M	0.697	0.22
57_A	117_H	0.696	0.22
56_A	81_V	0.694	0.22
101_E	115_V	0.690	0.22
46_L	88_E	0.688	0.22
134_K	138_A	0.688	0.22
38_M	113_K	0.684	0.22
25_F	60_A	0.681	0.22
93_M	113_K	0.678	0.22
54_G	82_F	0.677	0.22
7_E	120_P	0.676	0.22
106_S	130_E	0.676	0.22
31_A	78_T	0.668	0.21
26_E	77_N	0.661	0.21
17_R	29_T	0.659	0.21
71_N	74_T	0.656	0.21
111_K	142_A	0.655	0.21
51_S	104_S	0.651	0.21
55_C	104_S	0.651	0.21
110_L	116_V	0.650	0.20
92_K	96_Y	0.642	0.20
33_E	76_D	0.640	0.20
38_M	114_E	0.639	0.20
63_A	129_M	0.638	0.20
115_V	118_F	0.637	0.20
127_H	133_M	0.635	0.20
47_V	110_L	0.635	0.20
33_E	95_E	0.634	0.20
12_L	127_H	0.632	0.20
9_M	106_S	0.632	0.20
22_G	70_Q	0.631	0.20
57_A	139_A	0.627	0.20
45_T	114_E	0.621	0.19
31_A	126_G	0.620	0.19
47_V	76_D	0.613	0.19
120_P	123_E	0.612	0.19
15_P	20_L	0.606	0.19
42_E	74_T	0.605	0.19
79_V	126_G	0.600	0.19
128_D	131_E	0.592	0.18
110_L	142_A	0.588	0.18
53_C	83_A	0.588	0.18
83_A	104_S	0.587	0.18
33_E	38_M	0.584	0.18
82_F	94_R	0.580	0.18
35_E	95_E	0.579	0.18
23_A	79_V	0.577	0.18
37_F	113_K	0.576	0.18
10_R	93_M	0.576	0.18
37_F	77_N	0.573	0.18
37_F	79_V	0.571	0.18
116_V	135_N	0.567	0.17
39_E	113_K	0.565	0.17
69_L	74_T	0.556	0.17
48_V	130_E	0.554	0.17
93_M	120_P	0.553	0.17
26_E	138_A	0.551	0.17
28_L	60_A	0.548	0.17
110_L	123_E	0.548	0.17
33_E	90_T	0.546	0.17
66_Q	72_D	0.545	0.17
25_F	59_L	0.545	0.17
59_L	63_A	0.538	0.16
43_G	76_D	0.537	0.16
86_D	96_Y	0.528	0.16
7_E	15_P	0.527	0.16
18_R	88_E	0.526	0.16
130_E	137_T	0.520	0.16
51_S	54_G	0.518	0.16
76_D	79_V	0.517	0.16
58_G	85_Q	0.517	0.16
43_G	93_M	0.515	0.16
7_E	101_E	0.513	0.16
93_M	119_I	0.508	0.16
55_C	82_F	0.506	0.15
51_S	82_F	0.506	0.15
15_P	57_A	0.504	0.15
14_V	137_T	0.503	0.15
119_I	123_E	0.502	0.15
73_K	76_D	0.501	0.15
42_E	76_D	0.501	0.15
21_T	116_V	0.500	0.15

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
3fhkA	4	1	100	0.009	Contact Map
4euyA	1	0.5764	94	0.923	Contact Map
2j23A	1	0.7639	92.2	0.927	Contact Map
1ep7A	1	0.7431	91.3	0.929	Contact Map
4oo4A	2	0.7083	91.2	0.929	Contact Map
4i8bA	2	0.7083	91	0.929	Contact Map
2qgvA	2	0.8056	89.2	0.932	Contact Map
2yoiA	1	0.7153	88.7	0.933	Contact Map
1xwbA	2	0.7153	88.6	0.933	Contact Map
2oe3A	2	0.7292	87.4	0.934	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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