YPUI - BACSU - GREMLIN Contacts

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YPUI - Uncharacterized protein YpuI

UniProt:	P35156	Sequences: MKEAKCERQIHEGKIPNEMGHSIVRAQTQKTGEFLSMVVNTVNDYLNQTTLESLQAELPIEKGYCCDVLSTLRRMAVFCEGGAEACRRLLMQEPFQEARAEKTLYNVYHQCIEEFFMPKKDTWCENSRASYTGVSAIEFYHAVPASLEQLLLPLSAAFLKMREELAHYEASGSSMAPIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	179 (155)
Sequences:	103 (76)
Seq/√Len:	6.1

BACSU - YPUI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_N	76_A	3.001	0.79
79_C	82_G	2.818	0.74
89_L	103_T	2.649	0.69
70_S	80_E	2.592	0.67
65_C	69_L	2.530	0.65
69_L	78_F	2.369	0.60
74_R	96_Q	2.296	0.57
106_N	114_E	2.220	0.55
32_G	66_C	2.183	0.53
31_T	107_V	2.149	0.52
51_L	69_L	2.121	0.51
87_R	167_H	2.096	0.50
93_E	99_R	2.053	0.49
158_F	164_E	2.008	0.47
68_V	96_Q	1.911	0.44
53_S	59_P	1.873	0.42
43_N	66_C	1.847	0.41
51_L	88_R	1.774	0.39
105_Y	133_G	1.768	0.39
48_Q	52_E	1.734	0.38
29_Q	108_Y	1.727	0.37
42_V	111_C	1.716	0.37
95_F	132_T	1.697	0.36
68_V	155_S	1.671	0.35
142_A	145_A	1.618	0.34
98_A	167_H	1.612	0.34
154_L	158_F	1.591	0.33
68_V	151_L	1.588	0.33
86_C	112_I	1.570	0.32
139_F	151_L	1.569	0.32
70_S	107_V	1.559	0.32
26_A	106_N	1.556	0.32
61_E	141_H	1.525	0.31
22_S	42_V	1.519	0.31
20_G	93_E	1.480	0.29
37_M	151_L	1.461	0.29
24_V	130_S	1.452	0.29
36_S	87_R	1.439	0.28
79_C	170_A	1.432	0.28
84_E	117_M	1.428	0.28
56_A	99_R	1.416	0.28
21_H	170_A	1.411	0.27
37_M	59_P	1.403	0.27
67_D	76_A	1.389	0.27
31_T	164_E	1.368	0.26
54_L	69_L	1.365	0.26
84_E	88_R	1.361	0.26
79_C	94_P	1.344	0.26
72_L	103_T	1.323	0.25
76_A	80_E	1.311	0.25
70_S	106_N	1.299	0.24
46_L	111_C	1.299	0.24
45_Y	53_S	1.293	0.24
45_Y	69_L	1.288	0.24
45_Y	60_I	1.287	0.24
20_G	114_E	1.271	0.24
68_V	143_V	1.268	0.24
43_N	116_F	1.245	0.23
30_K	96_Q	1.243	0.23
43_N	70_S	1.239	0.23
92_Q	156_A	1.233	0.23
101_E	168_Y	1.225	0.22
142_A	147_L	1.221	0.22
75_M	172_G	1.209	0.22
45_Y	150_L	1.200	0.22
43_N	142_A	1.195	0.22
145_A	149_Q	1.168	0.21
72_L	100_A	1.154	0.21
29_Q	148_E	1.136	0.20
97_E	114_E	1.121	0.20
143_V	161_M	1.117	0.20
32_G	58_L	1.115	0.20
64_Y	136_A	1.102	0.20
36_S	120_K	1.088	0.19
44_D	62_K	1.081	0.19
123_W	127_S	1.076	0.19
67_D	145_A	1.075	0.19
41_T	147_L	1.073	0.19
99_R	170_A	1.066	0.19
40_N	149_Q	1.059	0.19
123_W	159_L	1.057	0.19
102_K	114_E	1.053	0.18
89_L	141_H	1.046	0.18
30_K	43_N	1.038	0.18
127_S	159_L	1.037	0.18
27_Q	114_E	1.020	0.18
40_N	44_D	1.019	0.18
54_L	120_K	1.009	0.18
78_F	142_A	1.004	0.17
81_G	155_S	1.004	0.17
155_S	159_L	1.002	0.17
70_S	113_E	0.976	0.17
121_D	127_S	0.975	0.17
45_Y	84_E	0.964	0.17
42_V	72_L	0.958	0.16
59_P	140_Y	0.955	0.16
43_N	96_Q	0.945	0.16
37_M	141_H	0.937	0.16
37_M	107_V	0.929	0.16
98_A	156_A	0.926	0.16
119_K	172_G	0.920	0.16
108_Y	133_G	0.917	0.16
107_V	115_F	0.915	0.16
27_Q	155_S	0.909	0.16
54_L	91_M	0.908	0.16
40_N	63_G	0.905	0.15
38_V	42_V	0.902	0.15
121_D	159_L	0.901	0.15
68_V	74_R	0.899	0.15
40_N	164_E	0.890	0.15
33_E	72_L	0.875	0.15
95_F	109_H	0.868	0.15
61_E	72_L	0.865	0.15
21_H	114_E	0.864	0.15
55_Q	58_L	0.863	0.15
24_V	82_G	0.858	0.15
65_C	133_G	0.815	0.14
68_V	163_E	0.804	0.14
28_T	68_V	0.798	0.14
21_H	93_E	0.792	0.13
138_E	173_S	0.786	0.13
70_S	158_F	0.784	0.13
65_C	105_Y	0.779	0.13
36_S	45_Y	0.773	0.13
123_W	129_A	0.773	0.13
50_T	100_A	0.771	0.13
30_K	50_T	0.761	0.13
31_T	117_M	0.760	0.13
29_Q	134_V	0.758	0.13
32_G	51_L	0.758	0.13
111_C	158_F	0.757	0.13
39_V	79_C	0.757	0.13
57_E	60_I	0.752	0.13
42_V	164_E	0.750	0.13
64_Y	142_A	0.750	0.13
111_C	122_T	0.733	0.13
142_A	149_Q	0.731	0.12
65_C	88_R	0.721	0.12
22_S	63_G	0.720	0.12
37_M	63_G	0.719	0.12
50_T	143_V	0.719	0.12
55_Q	63_G	0.714	0.12
83_A	159_L	0.711	0.12
123_W	155_S	0.709	0.12
111_C	147_L	0.708	0.12
108_Y	119_K	0.704	0.12
90_L	147_L	0.700	0.12
46_L	140_Y	0.700	0.12
67_D	161_M	0.697	0.12
72_L	153_P	0.695	0.12
60_I	65_C	0.695	0.12
62_K	145_A	0.691	0.12
68_V	154_L	0.690	0.12
88_R	99_R	0.690	0.12
44_D	149_Q	0.683	0.12
34_F	154_L	0.680	0.12
81_G	159_L	0.679	0.12
24_V	89_L	0.679	0.12
130_S	138_E	0.677	0.12
121_D	129_A	0.676	0.12
155_S	163_E	0.676	0.12
23_I	28_T	0.675	0.12
71_T	134_V	0.656	0.11
59_P	112_I	0.653	0.11
94_P	105_Y	0.653	0.11
89_L	110_Q	0.652	0.11
49_T	160_K	0.648	0.11
36_S	83_A	0.646	0.11
96_Q	124_C	0.646	0.11
66_C	116_F	0.627	0.11
41_T	146_S	0.623	0.11
28_T	84_E	0.623	0.11
101_E	165_L	0.617	0.11
38_V	54_L	0.609	0.11
26_A	58_L	0.608	0.11
62_K	155_S	0.607	0.11
62_K	98_A	0.606	0.11
123_W	163_E	0.604	0.11
40_N	56_A	0.604	0.11
89_L	102_K	0.603	0.11
37_M	52_E	0.602	0.11
105_Y	119_K	0.600	0.11
25_R	111_C	0.599	0.11
33_E	48_Q	0.597	0.11
24_V	110_Q	0.595	0.10
84_E	107_V	0.595	0.10
51_L	133_G	0.594	0.10
126_N	138_E	0.594	0.10
67_D	87_R	0.592	0.10
96_Q	151_L	0.589	0.10
64_Y	78_F	0.588	0.10
79_C	158_F	0.586	0.10
59_P	89_L	0.586	0.10
30_K	90_L	0.585	0.10
51_L	65_C	0.585	0.10
157_A	164_E	0.583	0.10
109_H	168_Y	0.582	0.10
25_R	154_L	0.577	0.10
39_V	48_Q	0.571	0.10
83_A	129_A	0.569	0.10
86_C	106_N	0.567	0.10
41_T	112_I	0.565	0.10
80_E	132_T	0.558	0.10
40_N	48_Q	0.557	0.10
50_T	122_T	0.553	0.10
78_F	91_M	0.552	0.10
138_E	170_A	0.550	0.10
26_A	99_R	0.550	0.10
102_K	143_V	0.544	0.10
89_L	150_L	0.541	0.10
29_Q	107_V	0.540	0.10
102_K	142_A	0.537	0.10
129_A	135_S	0.532	0.10
31_T	136_A	0.527	0.10
45_Y	79_C	0.527	0.10
27_Q	123_W	0.526	0.10
121_D	163_E	0.525	0.10
71_T	83_A	0.523	0.10
115_F	137_I	0.523	0.10
30_K	117_M	0.521	0.10
120_K	172_G	0.519	0.10
55_Q	153_P	0.518	0.09
147_L	152_L	0.516	0.09
86_C	113_E	0.515	0.09
132_T	171_S	0.514	0.09
27_Q	129_A	0.514	0.09
41_T	67_D	0.511	0.09
121_D	155_S	0.508	0.09
65_C	76_A	0.505	0.09
43_N	79_C	0.503	0.09
99_R	103_T	0.500	0.09
57_E	72_L	0.500	0.09

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
1ov9A	2	0.2123	9.4	0.969	Contact Map
4nqiA	2	0.6089	8.1	0.97	Contact Map
4wyqA	1	0.5754	7.9	0.97	Contact Map
1pd3A	2	0.2905	7.2	0.971	Contact Map
2y75A	5	0.3184	6.6	0.971	Contact Map
4aurA	1	0.4246	6.4	0.972	Contact Map
2k0mA	1	0.4972	6.3	0.972	Contact Map
3iqtA	1	0.2346	6	0.972	Contact Map
3zqsA	3	0.514	5.6	0.972	Contact Map
1gs9A	1	0.3184	4.9	0.973	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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