YHJR - BACSU - GREMLIN Contacts

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YHJR - Uncharacterized protein YhjR

UniProt:	O07572	Sequences: MHYSYYPYPVPYREDPVLIRNLQKAINGEFSAIQCYRKLAELAHSDEVRKQIEEIRRDEIRHLREFSTLYGSITGKHIMPKQTEECPDNFTRGLDAAFKDEQETVDFYLRAAEETSNLKAKGVFTRAARDEQNHAVWFLYYLMER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	145 (131)
Sequences:	221 (182)
Seq/√Len:	15.9

BACSU - YHJR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_L	93_G	3.966	1.00
29_E	131_E	3.472	0.99
36_Y	101_E	2.700	0.97
98_F	142_L	2.506	0.95
90_F	94_L	2.318	0.92
122_G	125_T	2.191	0.90
59_E	134_H	2.160	0.89
48_V	90_F	2.106	0.88
133_N	137_W	2.103	0.88
22_L	73_I	2.085	0.87
94_L	141_Y	2.031	0.86
123_V	127_A	1.996	0.85
55_I	87_P	1.926	0.82
106_D	133_N	1.912	0.82
65_E	123_V	1.899	0.81
59_E	104_T	1.890	0.81
25_A	66_F	1.864	0.80
55_I	133_N	1.855	0.80
132_Q	136_V	1.835	0.79
62_H	130_D	1.805	0.78
102_Q	106_D	1.780	0.77
84_E	87_P	1.758	0.76
124_F	127_A	1.595	0.69
45_S	48_V	1.572	0.67
30_F	34_Q	1.549	0.66
124_F	128_A	1.548	0.66
47_E	99_K	1.532	0.65
43_A	90_F	1.515	0.64
18_L	115_T	1.497	0.63
109_L	126_R	1.412	0.59
32_A	100_D	1.341	0.55
136_V	139_L	1.339	0.55
44_H	118_L	1.308	0.53
47_E	95_D	1.288	0.52
115_T	124_F	1.286	0.52
41_E	45_S	1.278	0.51
113_E	126_R	1.277	0.51
71_G	77_H	1.276	0.51
56_R	87_P	1.269	0.51
58_D	130_D	1.244	0.49
106_D	137_W	1.239	0.49
90_F	141_Y	1.235	0.49
58_D	134_H	1.192	0.46
130_D	134_H	1.190	0.46
58_D	135_A	1.184	0.46
37_R	41_E	1.152	0.44
75_G	93_G	1.132	0.43
42_L	90_F	1.130	0.43
29_E	32_A	1.107	0.41
106_D	122_G	1.093	0.41
62_H	134_H	1.081	0.40
49_R	85_E	1.075	0.40
63_L	142_L	1.073	0.39
33_I	63_L	1.071	0.39
125_T	128_A	1.068	0.39
103_E	141_Y	1.068	0.39
29_E	66_F	1.064	0.39
55_I	134_H	1.051	0.38
102_Q	135_A	1.051	0.38
59_E	62_H	1.050	0.38
37_R	64_R	1.040	0.38
28_G	101_E	1.034	0.37
30_F	63_L	1.033	0.37
66_F	131_E	1.030	0.37
24_K	61_R	1.028	0.37
38_K	84_E	1.027	0.37
14_E	76_K	1.016	0.36
16_P	41_E	1.007	0.36
54_E	133_N	1.000	0.35
102_Q	137_W	0.999	0.35
25_A	32_A	0.991	0.35
18_L	114_E	0.980	0.34
104_T	130_D	0.973	0.34
50_K	53_E	0.959	0.33
19_I	123_V	0.956	0.33
91_T	142_L	0.950	0.33
57_R	89_N	0.950	0.33
35_C	109_L	0.929	0.32
45_S	67_S	0.926	0.32
41_E	92_R	0.923	0.31
35_C	106_D	0.922	0.31
20_R	95_D	0.921	0.31
29_E	101_E	0.911	0.31
20_R	61_R	0.911	0.31
29_E	108_Y	0.910	0.31
25_A	134_H	0.907	0.31
22_L	109_L	0.899	0.30
132_Q	139_L	0.899	0.30
52_I	135_A	0.897	0.30
76_K	103_E	0.896	0.30
23_Q	78_I	0.895	0.30
110_R	122_G	0.894	0.30
47_E	92_R	0.877	0.29
64_R	68_T	0.876	0.29
45_S	68_T	0.869	0.29
47_E	51_Q	0.856	0.28
30_F	33_I	0.854	0.28
35_C	86_C	0.853	0.28
102_Q	109_L	0.848	0.28
26_I	106_D	0.848	0.28
39_L	90_F	0.836	0.27
16_P	125_T	0.833	0.27
69_L	120_A	0.826	0.27
64_R	103_E	0.822	0.27
46_D	50_K	0.816	0.26
104_T	140_Y	0.813	0.26
35_C	104_T	0.800	0.26
128_A	132_Q	0.792	0.25
102_Q	139_L	0.792	0.25
27_N	78_I	0.786	0.25
14_E	122_G	0.783	0.25
71_G	123_V	0.781	0.25
26_I	115_T	0.776	0.25
63_L	80_P	0.774	0.25
125_T	129_R	0.771	0.24
52_I	66_F	0.764	0.24
88_D	121_K	0.764	0.24
72_S	128_A	0.762	0.24
89_N	92_R	0.760	0.24
57_R	79_M	0.760	0.24
42_L	89_N	0.750	0.24
22_L	69_L	0.742	0.23
28_G	59_E	0.742	0.23
33_I	97_A	0.742	0.23
121_K	125_T	0.736	0.23
112_A	125_T	0.734	0.23
22_L	76_K	0.732	0.23
28_G	66_F	0.731	0.23
49_R	88_D	0.729	0.23
55_I	137_W	0.722	0.22
33_I	60_I	0.717	0.22
24_K	53_E	0.708	0.22
21_N	107_F	0.706	0.22
28_G	104_T	0.701	0.22
59_E	130_D	0.698	0.21
59_E	100_D	0.694	0.21
112_A	121_K	0.685	0.21
53_E	57_R	0.683	0.21
86_C	132_Q	0.683	0.21
125_T	133_N	0.678	0.21
109_L	113_E	0.677	0.21
28_G	36_Y	0.670	0.20
107_F	128_A	0.664	0.20
128_A	137_W	0.661	0.20
107_F	138_F	0.659	0.20
82_Q	116_S	0.658	0.20
71_G	78_I	0.654	0.20
22_L	111_A	0.648	0.20
56_R	60_I	0.645	0.19
50_K	90_F	0.643	0.19
22_L	77_H	0.639	0.19
51_Q	141_Y	0.636	0.19
73_I	122_G	0.636	0.19
92_R	123_V	0.633	0.19
80_P	98_F	0.629	0.19
78_I	95_D	0.629	0.19
43_A	70_Y	0.628	0.19
55_I	138_F	0.626	0.19
32_A	138_F	0.623	0.19
12_Y	88_D	0.622	0.19
61_R	126_R	0.620	0.19
21_N	129_R	0.615	0.18
35_C	134_H	0.609	0.18
112_A	122_G	0.604	0.18
25_A	59_E	0.598	0.18
56_R	59_E	0.594	0.18
87_P	93_G	0.588	0.17
62_H	108_Y	0.587	0.17
78_I	103_E	0.581	0.17
19_I	79_M	0.574	0.17
68_T	85_E	0.569	0.17
78_I	133_N	0.566	0.17
101_E	104_T	0.564	0.17
45_S	95_D	0.563	0.17
87_P	94_L	0.559	0.17
76_K	88_D	0.552	0.16
44_H	90_F	0.552	0.16
63_L	105_V	0.551	0.16
49_R	129_R	0.549	0.16
16_P	45_S	0.545	0.16
14_E	116_S	0.543	0.16
113_E	128_A	0.541	0.16
52_I	138_F	0.540	0.16
79_M	98_F	0.538	0.16
14_E	142_L	0.534	0.16
54_E	58_D	0.532	0.16
34_Q	38_K	0.532	0.16
29_E	36_Y	0.524	0.15
71_G	115_T	0.523	0.15
74_T	131_E	0.523	0.15
98_F	102_Q	0.515	0.15
111_A	130_D	0.508	0.15
85_E	96_A	0.506	0.15
32_A	101_E	0.504	0.15
50_K	89_N	0.503	0.15
109_L	129_R	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
2fzfA	2	0.9517	99.6	0.663	Contact Map
1vjxA	1	0.9172	99.5	0.668	Contact Map
2oh3A	2	0.8828	99.5	0.68	Contact Map
4etrA	1	0.8276	99.2	0.729	Contact Map
4di0A	2	0.9034	99.1	0.733	Contact Map
4am5A	6	0.9241	99.1	0.74	Contact Map
1j30A	5	0.9034	99	0.746	Contact Map
3qhbA	1	1	99	0.747	Contact Map
1yuzA	2	1	98.9	0.752	Contact Map
1lkoA	3	0.9103	98.9	0.752	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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