YPIB - BACSU - GREMLIN Contacts

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YPIB - UPF0302 protein YpiB

UniProt:	P54390	Sequences: MQTPVSVNEKKDFIRWFLNHYQLKRRECVWILNYLMSHDSLMEKVHFVEQAEFCPRGIIMSTHCVEEVPFRFYKENVMTTDAEKSFHDIRLNKQQDLFIQLNFRSAYSSPEYAAVLESNPHIPKNLFENKKDQGLAEQILEHAISTFQREKLLKDIDDALDRHDKEAFEQLSRQLNQLT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	179 (174)
Sequences:	219 (169)
Seq/√Len:	12.8

BACSU - YPIB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_H	57_G	3.772	0.99
31_I	38_H	3.332	0.98
79_T	84_K	3.136	0.97
167_A	170_Q	2.875	0.95
26_R	30_W	2.733	0.94
158_D	162_R	2.723	0.94
54_C	100_Q	2.632	0.93
70_F	85_S	2.614	0.92
5_V	130_K	2.603	0.92
17_F	23_L	2.327	0.87
61_S	101_L	2.246	0.85
164_D	167_A	2.166	0.83
108_S	152_L	2.153	0.82
87_H	91_L	1.975	0.76
9_E	37_S	1.953	0.75
165_K	169_E	1.897	0.73
44_K	99_I	1.896	0.73
47_F	157_D	1.852	0.71
158_D	167_A	1.848	0.71
50_Q	127_F	1.840	0.71
92_N	157_D	1.809	0.70
152_L	174_Q	1.790	0.69
57_G	93_K	1.763	0.67
86_F	90_R	1.743	0.67
87_H	90_R	1.720	0.65
23_L	101_L	1.700	0.65
23_L	70_F	1.698	0.64
14_I	109_S	1.684	0.64
173_R	177_Q	1.661	0.63
18_L	101_L	1.616	0.60
162_R	174_Q	1.599	0.60
17_F	73_Y	1.597	0.60
74_K	90_R	1.587	0.59
169_E	172_S	1.578	0.59
93_K	97_L	1.569	0.58
107_Y	113_A	1.543	0.57
35_L	90_R	1.531	0.56
33_N	140_L	1.521	0.56
84_K	88_D	1.514	0.55
18_L	136_A	1.486	0.54
11_K	26_R	1.481	0.54
9_E	61_S	1.478	0.53
39_D	147_F	1.477	0.53
42_M	65_V	1.438	0.51
70_F	101_L	1.431	0.51
149_R	166_E	1.408	0.50
23_L	85_S	1.406	0.50
49_E	116_L	1.400	0.49
39_D	96_D	1.398	0.49
30_W	90_R	1.387	0.49
14_I	77_V	1.371	0.48
149_R	153_L	1.370	0.48
80_T	89_I	1.370	0.48
37_S	41_L	1.356	0.47
142_H	146_T	1.339	0.46
128_E	165_K	1.339	0.46
141_E	170_Q	1.296	0.44
153_L	175_L	1.295	0.44
93_K	100_Q	1.294	0.44
30_W	83_E	1.282	0.43
161_D	175_L	1.263	0.42
134_G	167_A	1.259	0.42
93_K	139_I	1.258	0.42
158_D	166_E	1.258	0.42
149_R	177_Q	1.207	0.40
63_H	76_N	1.203	0.39
21_Y	102_N	1.200	0.39
72_F	103_F	1.173	0.38
55_P	119_N	1.165	0.37
58_I	95_Q	1.163	0.37
64_C	80_T	1.154	0.37
59_I	130_K	1.144	0.36
27_E	86_F	1.142	0.36
17_F	103_F	1.141	0.36
17_F	59_I	1.135	0.36
41_L	44_K	1.118	0.35
36_M	65_V	1.118	0.35
148_Q	151_K	1.116	0.35
9_E	65_V	1.102	0.34
27_E	90_R	1.096	0.34
29_V	56_R	1.089	0.34
143_A	147_F	1.071	0.33
15_R	19_N	1.068	0.33
51_A	58_I	1.054	0.32
45_V	72_F	1.052	0.32
79_T	161_D	1.050	0.32
23_L	41_L	1.049	0.32
131_K	173_R	1.043	0.32
108_S	155_D	1.040	0.32
142_H	145_S	1.039	0.32
30_W	33_N	1.006	0.30
47_F	61_S	0.996	0.30
111_E	148_Q	0.980	0.29
7_V	65_V	0.976	0.29
60_M	149_R	0.975	0.29
26_R	84_K	0.969	0.28
55_P	121_H	0.964	0.28
64_C	104_R	0.962	0.28
90_R	120_P	0.959	0.28
166_E	169_E	0.954	0.28
33_N	37_S	0.933	0.27
29_V	82_A	0.932	0.27
5_V	174_Q	0.927	0.27
110_P	113_A	0.924	0.27
29_V	73_Y	0.912	0.26
27_E	117_E	0.912	0.26
23_L	83_E	0.901	0.26
31_I	157_D	0.895	0.25
155_D	171_L	0.895	0.25
151_K	173_R	0.888	0.25
150_E	177_Q	0.888	0.25
71_R	127_F	0.880	0.25
162_R	173_R	0.876	0.25
35_L	116_L	0.876	0.25
37_S	96_D	0.874	0.25
100_Q	132_D	0.863	0.24
46_H	98_F	0.862	0.24
51_A	100_Q	0.860	0.24
11_K	71_R	0.856	0.24
9_E	98_F	0.836	0.23
87_H	119_N	0.835	0.23
18_L	61_S	0.833	0.23
85_S	102_N	0.831	0.23
146_T	154_K	0.825	0.23
11_K	34_Y	0.813	0.22
27_E	69_P	0.811	0.22
56_R	71_R	0.809	0.22
34_Y	119_N	0.802	0.22
151_K	155_D	0.791	0.22
5_V	141_E	0.790	0.22
44_K	60_M	0.788	0.21
110_P	158_D	0.787	0.21
49_E	67_E	0.782	0.21
72_F	88_D	0.780	0.21
7_V	150_E	0.777	0.21
54_C	87_H	0.777	0.21
72_F	101_L	0.770	0.21
5_V	107_Y	0.765	0.21
30_W	81_D	0.761	0.21
21_Y	64_C	0.757	0.20
135_L	139_I	0.751	0.20
24_K	28_C	0.749	0.20
76_N	126_L	0.748	0.20
15_R	25_R	0.747	0.20
25_R	72_F	0.746	0.20
44_K	96_D	0.746	0.20
20_H	31_I	0.744	0.20
96_D	108_S	0.740	0.20
26_R	81_D	0.739	0.20
162_R	170_Q	0.738	0.20
5_V	76_N	0.737	0.20
61_S	99_I	0.737	0.20
25_R	31_I	0.734	0.20
35_L	51_A	0.734	0.20
63_H	151_K	0.733	0.20
97_L	177_Q	0.733	0.20
165_K	168_F	0.731	0.20
33_N	46_H	0.729	0.19
9_E	12_D	0.723	0.19
82_A	123_P	0.717	0.19
71_R	136_A	0.708	0.19
11_K	92_N	0.706	0.19
76_N	161_D	0.695	0.18
25_R	59_I	0.695	0.18
31_I	82_A	0.694	0.18
61_S	70_F	0.692	0.18
112_Y	115_V	0.690	0.18
163_H	174_Q	0.686	0.18
46_H	119_N	0.685	0.18
56_R	77_V	0.685	0.18
52_E	125_N	0.682	0.18
154_K	158_D	0.681	0.18
60_M	164_D	0.680	0.18
27_E	30_W	0.673	0.18
84_K	161_D	0.672	0.18
49_E	124_K	0.669	0.18
172_S	175_L	0.669	0.18
68_V	82_A	0.667	0.18
118_S	153_L	0.665	0.17
149_R	158_D	0.665	0.17
58_I	92_N	0.663	0.17
102_N	132_D	0.661	0.17
65_V	105_S	0.661	0.17
48_V	168_F	0.656	0.17
57_G	75_E	0.650	0.17
8_N	93_K	0.644	0.17
41_L	124_K	0.636	0.17
52_E	77_V	0.635	0.17
17_F	175_L	0.633	0.17
140_L	166_E	0.630	0.16
83_E	101_L	0.629	0.16
52_E	104_R	0.628	0.16
108_S	176_N	0.624	0.16
21_Y	73_Y	0.619	0.16
87_H	121_H	0.613	0.16
58_I	121_H	0.609	0.16
66_E	91_L	0.605	0.16
30_W	87_H	0.605	0.16
56_R	112_Y	0.605	0.16
11_K	30_W	0.605	0.16
46_H	92_N	0.605	0.16
31_I	60_M	0.602	0.16
75_E	78_M	0.600	0.16
7_V	164_D	0.598	0.16
54_C	82_A	0.597	0.16
40_S	147_F	0.597	0.16
44_K	56_R	0.596	0.16
15_R	148_Q	0.595	0.15
134_G	137_E	0.592	0.15
122_I	133_Q	0.588	0.15
148_Q	174_Q	0.586	0.15
57_G	107_Y	0.585	0.15
155_D	167_A	0.583	0.15
101_L	136_A	0.581	0.15
83_E	136_A	0.578	0.15
126_L	132_D	0.578	0.15
77_V	169_E	0.577	0.15
59_I	161_D	0.577	0.15
30_W	119_N	0.575	0.15
26_R	86_F	0.574	0.15
41_L	97_L	0.574	0.15
55_P	123_P	0.571	0.15
77_V	93_K	0.571	0.15
107_Y	161_D	0.566	0.15
138_Q	141_E	0.564	0.15
151_K	154_K	0.562	0.15
12_D	142_H	0.559	0.15
22_Q	63_H	0.556	0.14
156_I	168_F	0.556	0.14
19_N	141_E	0.554	0.14
60_M	150_E	0.550	0.14
4_P	118_S	0.548	0.14
79_T	136_A	0.548	0.14
31_I	51_A	0.543	0.14
146_T	162_R	0.542	0.14
24_K	101_L	0.541	0.14
67_E	175_L	0.540	0.14
79_T	88_D	0.538	0.14
57_G	92_N	0.535	0.14
87_H	120_P	0.534	0.14
54_C	84_K	0.534	0.14
47_F	160_L	0.534	0.14
158_D	163_H	0.533	0.14
40_S	176_N	0.530	0.14
73_Y	175_L	0.530	0.14
54_C	79_T	0.529	0.14
139_I	151_K	0.528	0.14
39_D	92_N	0.527	0.14
26_R	33_N	0.527	0.14
90_R	119_N	0.525	0.14
17_F	45_V	0.525	0.14
19_N	92_N	0.518	0.14
99_I	163_H	0.515	0.13
8_N	43_E	0.507	0.13
74_K	83_E	0.506	0.13
30_W	89_I	0.506	0.13
20_H	97_L	0.503	0.13
96_D	126_L	0.501	0.13
46_H	55_P	0.501	0.13
20_H	105_S	0.500	0.13
32_L	103_F	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
3do9A	1	0.9888	100	0.098	Contact Map
1gp8A	1	0.2235	54	0.943	Contact Map
2fztA	2	0.1899	27.6	0.952	Contact Map
3pehA	2	0.3296	13.3	0.958	Contact Map
2jk1A	2	0.7039	12.1	0.959	Contact Map
2r6aC	1	0.7318	9.1	0.961	Contact Map
1t5qA	1	0.1173	8.2	0.962	Contact Map
2kjgA	1	0.3743	7.7	0.962	Contact Map
1wjtA	1	0.2458	7.6	0.962	Contact Map
1u2zA	1	0.6927	7.4	0.962	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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