YRHD - BACSU - GREMLIN Contacts

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YRHD - Uncharacterized protein YrhD

UniProt:	O05396	Sequences: MATPITTIKKETKTAEQIKLEKIEELKELLAENEDAVSKTMTLMNELNDLGIFDAATSMLRAKEDIAKIALGQVSREPVTNLINTMMAAGGALTKADPEFTAKLLESVMAGTEQAQSFLKEDKKVGILDLLKAMNDPDINRAVGFGLQFLKGMGKELREQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (156)
Sequences:	199 (161)
Seq/√Len:	12.9

BACSU - YRHD YJGD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_M	66_I	5.777	1.00
13_K	21_E	3.393	0.98
36_A	56_A	3.015	0.97
114_Q	155_K	3.003	0.97
69_I	73_Q	2.783	0.95
26_L	38_S	2.758	0.94
40_T	44_M	2.639	0.93
142_A	153_M	2.577	0.92
136_D	151_K	2.576	0.92
18_I	22_K	2.303	0.87
21_E	143_V	2.256	0.85
35_D	127_I	2.217	0.84
125_V	144_G	2.214	0.84
62_A	84_N	2.134	0.82
29_L	38_S	2.101	0.81
26_L	37_V	2.079	0.80
111_G	152_G	1.978	0.77
149_F	153_M	1.953	0.76
39_K	48_N	1.782	0.69
50_L	133_A	1.763	0.68
96_A	126_G	1.712	0.65
60_L	74_V	1.705	0.65
64_E	67_A	1.702	0.65
47_L	60_L	1.593	0.59
31_A	156_E	1.575	0.59
15_A	19_K	1.554	0.58
3_T	71_L	1.527	0.56
22_K	44_M	1.526	0.56
50_L	63_K	1.476	0.54
101_T	151_K	1.430	0.51
138_D	151_K	1.400	0.50
140_N	143_V	1.391	0.49
10_K	28_E	1.388	0.49
4_P	154_G	1.374	0.48
83_I	123_K	1.356	0.47
19_K	28_E	1.346	0.47
41_M	127_I	1.346	0.47
28_E	35_D	1.342	0.47
43_L	74_V	1.333	0.46
108_V	153_M	1.326	0.46
71_L	115_A	1.305	0.45
108_V	131_L	1.304	0.45
129_D	139_I	1.294	0.44
85_T	96_A	1.278	0.43
47_L	53_F	1.261	0.42
84_N	101_T	1.259	0.42
97_D	104_L	1.255	0.42
141_R	150_L	1.255	0.42
28_E	43_L	1.234	0.41
90_G	94_T	1.231	0.41
39_K	54_D	1.224	0.41
115_A	148_Q	1.202	0.39
8_I	99_E	1.187	0.39
80_T	151_K	1.181	0.38
56_A	135_N	1.177	0.38
81_N	100_F	1.175	0.38
142_A	145_F	1.171	0.38
17_Q	108_V	1.149	0.37
56_A	143_V	1.135	0.36
60_L	112_T	1.121	0.35
63_K	67_A	1.119	0.35
27_K	92_A	1.114	0.35
73_Q	76_R	1.100	0.34
50_L	55_A	1.099	0.34
20_L	23_I	1.091	0.34
76_R	79_V	1.087	0.34
48_N	130_L	1.084	0.34
63_K	84_N	1.076	0.33
64_E	78_P	1.051	0.32
1_M	8_I	1.041	0.32
123_K	127_I	1.028	0.31
89_A	94_T	1.019	0.31
83_I	97_D	1.016	0.31
143_V	147_L	1.000	0.30
64_E	134_M	0.997	0.30
83_I	99_E	0.990	0.29
40_T	58_S	0.986	0.29
3_T	18_I	0.969	0.29
22_K	29_L	0.968	0.29
42_T	127_I	0.964	0.28
3_T	113_E	0.956	0.28
41_M	52_I	0.948	0.28
107_S	152_G	0.947	0.28
44_M	83_I	0.944	0.28
12_T	58_S	0.942	0.27
83_I	136_D	0.937	0.27
10_K	49_D	0.935	0.27
40_T	129_D	0.934	0.27
85_T	94_T	0.920	0.27
82_L	153_M	0.915	0.26
101_T	143_V	0.915	0.26
34_E	105_L	0.915	0.26
27_K	67_A	0.914	0.26
64_E	135_N	0.911	0.26
26_L	34_E	0.910	0.26
38_S	83_I	0.897	0.26
72_G	89_A	0.897	0.26
3_T	59_M	0.891	0.25
137_P	154_G	0.891	0.25
100_F	113_E	0.890	0.25
14_T	143_V	0.888	0.25
44_M	106_E	0.886	0.25
33_N	49_D	0.882	0.25
13_K	17_Q	0.879	0.25
26_L	138_D	0.871	0.25
70_A	76_R	0.869	0.25
24_E	28_E	0.860	0.24
54_D	57_T	0.858	0.24
25_E	108_V	0.856	0.24
59_M	148_Q	0.847	0.24
59_M	132_K	0.847	0.24
125_V	140_N	0.846	0.24
1_M	5_I	0.834	0.23
54_D	61_R	0.832	0.23
24_E	147_L	0.831	0.23
111_G	153_M	0.830	0.23
4_P	84_N	0.830	0.23
76_R	80_T	0.825	0.23
26_L	36_A	0.821	0.23
98_P	101_T	0.820	0.23
51_G	128_L	0.818	0.23
35_D	126_G	0.815	0.23
33_N	135_N	0.813	0.22
27_K	33_N	0.810	0.22
14_T	17_Q	0.803	0.22
17_Q	90_G	0.802	0.22
24_E	104_L	0.802	0.22
8_I	149_F	0.800	0.22
42_T	130_L	0.771	0.21
14_T	141_R	0.771	0.21
81_N	91_G	0.770	0.21
4_P	32_E	0.765	0.21
36_A	58_S	0.761	0.21
32_E	52_I	0.760	0.21
12_T	70_A	0.758	0.21
65_D	122_D	0.746	0.20
51_G	54_D	0.735	0.20
2_A	5_I	0.729	0.20
29_L	105_L	0.727	0.19
16_E	148_Q	0.725	0.19
37_V	112_T	0.721	0.19
124_K	139_I	0.719	0.19
130_L	133_A	0.716	0.19
38_S	127_I	0.716	0.19
52_I	110_A	0.715	0.19
34_E	138_D	0.712	0.19
55_A	67_A	0.706	0.19
37_V	152_G	0.705	0.19
124_K	140_N	0.701	0.19
30_L	149_F	0.697	0.19
2_A	8_I	0.694	0.18
97_D	111_G	0.691	0.18
12_T	126_G	0.685	0.18
17_Q	37_V	0.684	0.18
97_D	139_I	0.683	0.18
16_E	23_I	0.679	0.18
13_K	89_A	0.675	0.18
25_E	34_E	0.674	0.18
18_I	37_V	0.673	0.18
17_Q	83_I	0.669	0.18
31_A	73_Q	0.669	0.18
63_K	101_T	0.665	0.18
39_K	57_T	0.665	0.18
75_S	85_T	0.661	0.17
139_I	147_L	0.661	0.17
63_K	119_L	0.659	0.17
96_A	110_A	0.659	0.17
51_G	154_G	0.657	0.17
8_I	74_V	0.656	0.17
129_D	140_N	0.652	0.17
65_D	70_A	0.652	0.17
16_E	124_K	0.651	0.17
66_I	112_T	0.650	0.17
70_A	73_Q	0.648	0.17
13_K	143_V	0.647	0.17
25_E	29_L	0.640	0.17
55_A	60_L	0.636	0.17
5_I	17_Q	0.636	0.17
43_L	60_L	0.633	0.17
73_Q	92_A	0.633	0.17
52_I	101_T	0.633	0.17
41_M	139_I	0.633	0.17
32_E	113_E	0.631	0.17
46_E	70_A	0.617	0.16
86_M	95_K	0.614	0.16
99_E	137_P	0.614	0.16
65_D	117_S	0.612	0.16
51_G	69_I	0.612	0.16
32_E	39_K	0.605	0.16
58_S	137_P	0.604	0.16
129_D	151_K	0.603	0.16
74_V	126_G	0.602	0.16
33_N	41_M	0.600	0.16
2_A	154_G	0.600	0.16
7_T	85_T	0.599	0.16
45_N	48_N	0.595	0.16
19_K	27_K	0.593	0.15
55_A	66_I	0.582	0.15
117_S	155_K	0.579	0.15
38_S	123_K	0.578	0.15
55_A	63_K	0.577	0.15
36_A	74_V	0.571	0.15
84_N	146_G	0.570	0.15
105_L	145_F	0.570	0.15
70_A	81_N	0.569	0.15
47_L	141_R	0.566	0.15
7_T	52_I	0.562	0.15
35_D	123_K	0.559	0.15
70_A	92_A	0.558	0.15
8_I	153_M	0.553	0.14
134_M	139_I	0.550	0.14
75_S	94_T	0.548	0.14
30_L	116_Q	0.544	0.14
51_G	132_K	0.541	0.14
19_K	116_Q	0.538	0.14
62_A	155_K	0.537	0.14
34_E	135_N	0.535	0.14
13_K	26_L	0.535	0.14
127_I	131_L	0.524	0.14
29_L	94_T	0.523	0.14
25_E	146_G	0.518	0.14
5_I	45_N	0.516	0.13
63_K	150_L	0.516	0.13
7_T	14_T	0.515	0.13
45_N	65_D	0.512	0.13
117_S	143_V	0.511	0.13
139_I	154_G	0.511	0.13
6_T	141_R	0.508	0.13
34_E	94_T	0.503	0.13
112_T	116_Q	0.503	0.13
6_T	25_E	0.503	0.13
8_I	25_E	0.502	0.13
19_K	70_A	0.501	0.13
118_F	143_V	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
1pu6A	1	0.7125	41.5	0.929	Contact Map
3fxdA	1	0.2437	22.8	0.938	Contact Map
1k8kG	1	0.775	20.5	0.939	Contact Map
3s6iA	1	0.7812	18.7	0.94	Contact Map
3dadA	1	0.9375	14.5	0.943	Contact Map
2abkA	1	0.7125	13.9	0.944	Contact Map
4unfA	1	0.8187	12.2	0.945	Contact Map
1wa5C	1	0.9875	11	0.946	Contact Map
1h2vC	1	0.8125	10.1	0.947	Contact Map
2c2aA	2	0.725	9.7	0.947	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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