YNDM - BACSU - GREMLIN Contacts

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YNDM - Uncharacterized membrane protein YndM

UniProt:	O31816	Sequences: MTIMNGFELHYLSFVYAQEFSSKNNNLGGQMKHIIALASKIAFTLALLYVILDRVYHASFLSVMFIALFLGFVSYLSGDMLVLPRTNNITASLADFGLSFVILWVFVLTQTRNDFSPFGAALLSAACLTVFEYFFHRYLLKNVLDENFRNELSARDNTLQYQTEAADELFPETKEKHKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	179 (144)
Sequences:	119 (94)
Seq/√Len:	7.8

BACSU - YNDM YCBP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
75_Y	168_E	3.148	0.89
48_L	103_L	2.458	0.73
33_H	88_N	2.429	0.72
73_V	160_Q	2.395	0.71
48_L	66_I	2.330	0.69
71_G	87_N	2.323	0.69
104_W	125_A	2.302	0.68
33_H	75_Y	2.084	0.60
73_V	86_T	1.979	0.56
163_T	166_A	1.959	0.55
166_A	169_L	1.946	0.55
55_V	104_W	1.814	0.49
52_L	70_L	1.792	0.48
53_D	106_F	1.768	0.47
47_L	58_A	1.731	0.46
123_L	139_L	1.725	0.46
46_A	71_G	1.704	0.45
96_F	117_P	1.703	0.45
101_V	130_V	1.622	0.41
88_N	134_F	1.583	0.40
131_F	171_P	1.578	0.40
100_F	107_V	1.574	0.40
128_L	143_V	1.568	0.39
52_L	86_T	1.535	0.38
31_M	48_L	1.533	0.38
94_A	97_G	1.502	0.37
121_A	125_A	1.482	0.36
84_P	138_Y	1.477	0.36
71_G	131_F	1.445	0.35
53_D	56_Y	1.441	0.35
54_R	66_I	1.431	0.34
58_A	130_V	1.415	0.34
33_H	86_T	1.413	0.34
69_F	113_N	1.407	0.33
88_N	94_A	1.370	0.32
101_V	126_A	1.351	0.31
88_N	91_A	1.341	0.31
44_T	49_Y	1.335	0.31
58_A	106_F	1.334	0.31
112_R	127_C	1.333	0.31
47_L	71_G	1.330	0.31
63_V	110_Q	1.324	0.30
71_G	127_C	1.315	0.30
77_S	128_L	1.314	0.30
33_H	82_V	1.301	0.30
66_I	114_D	1.282	0.29
111_T	116_S	1.280	0.29
39_S	42_A	1.249	0.28
49_Y	161_Y	1.246	0.28
31_M	84_P	1.225	0.27
102_I	171_P	1.221	0.27
72_F	93_L	1.213	0.27
80_M	143_V	1.210	0.27
51_I	63_V	1.193	0.26
70_L	102_I	1.193	0.26
65_F	100_F	1.188	0.26
84_P	104_W	1.174	0.26
77_S	82_V	1.168	0.25
103_L	117_P	1.159	0.25
91_A	163_T	1.154	0.25
78_G	92_S	1.153	0.25
52_L	56_Y	1.153	0.25
167_D	170_F	1.148	0.25
54_R	72_F	1.147	0.25
36_A	55_V	1.143	0.25
39_S	72_F	1.135	0.24
65_F	116_S	1.122	0.24
48_L	135_F	1.119	0.24
106_F	109_T	1.105	0.23
90_T	124_S	1.103	0.23
65_F	111_T	1.102	0.23
86_T	99_S	1.097	0.23
58_A	118_F	1.089	0.23
82_V	90_T	1.083	0.23
123_L	153_S	1.077	0.23
82_V	131_F	1.077	0.23
67_A	112_R	1.061	0.22
41_I	49_Y	1.057	0.22
66_I	103_L	1.048	0.22
46_A	165_A	1.046	0.22
66_I	135_F	1.026	0.21
47_L	159_L	1.014	0.21
69_F	163_T	1.006	0.21
42_A	170_F	0.995	0.20
57_H	99_S	0.992	0.20
75_Y	167_D	0.992	0.20
156_D	160_Q	0.985	0.20
34_I	155_R	0.980	0.20
78_G	88_N	0.980	0.20
74_S	119_G	0.980	0.20
54_R	100_F	0.975	0.20
138_Y	143_V	0.971	0.20
55_V	98_L	0.969	0.20
72_F	144_L	0.967	0.20
51_I	118_F	0.965	0.20
124_S	166_A	0.956	0.19
114_D	119_G	0.953	0.19
64_M	143_V	0.952	0.19
127_C	157_N	0.949	0.19
87_N	108_L	0.948	0.19
51_I	114_D	0.935	0.19
77_S	126_A	0.931	0.19
77_S	167_D	0.924	0.19
111_T	118_F	0.922	0.19
62_S	149_R	0.921	0.19
57_H	148_F	0.914	0.18
133_Y	165_A	0.907	0.18
65_F	121_A	0.905	0.18
42_A	145_D	0.904	0.18
74_S	99_S	0.901	0.18
46_A	102_I	0.898	0.18
93_L	141_K	0.897	0.18
50_V	123_L	0.893	0.18
38_A	143_V	0.892	0.18
36_A	143_V	0.891	0.18
141_K	175_E	0.890	0.18
37_L	170_F	0.890	0.18
99_S	129_T	0.889	0.18
60_F	70_L	0.883	0.18
51_I	123_L	0.881	0.18
51_I	117_P	0.879	0.18
78_G	82_V	0.875	0.17
45_L	49_Y	0.875	0.17
124_S	167_D	0.872	0.17
72_F	137_R	0.855	0.17
58_A	113_N	0.853	0.17
69_F	93_L	0.833	0.16
70_L	165_A	0.824	0.16
149_R	173_T	0.815	0.16
46_A	70_L	0.813	0.16
75_Y	85_R	0.804	0.16
131_F	165_A	0.795	0.16
74_S	137_R	0.791	0.16
65_F	157_N	0.789	0.15
67_A	127_C	0.788	0.15
97_G	162_Q	0.781	0.15
61_L	115_F	0.754	0.15
97_G	125_A	0.747	0.15
166_A	171_P	0.737	0.14
87_N	169_L	0.733	0.14
40_K	132_E	0.732	0.14
41_I	56_Y	0.726	0.14
120_A	135_F	0.717	0.14
70_L	162_Q	0.716	0.14
130_V	157_N	0.716	0.14
53_D	58_A	0.714	0.14
43_F	131_F	0.704	0.14
117_P	129_T	0.703	0.14
53_D	66_I	0.698	0.14
84_P	143_V	0.695	0.14
65_F	105_V	0.692	0.14
87_N	160_Q	0.678	0.13
106_F	116_S	0.678	0.13
33_H	115_F	0.677	0.13
47_L	87_N	0.674	0.13
55_V	67_A	0.668	0.13
46_A	56_Y	0.666	0.13
36_A	144_L	0.658	0.13
78_G	95_D	0.658	0.13
94_A	131_F	0.653	0.13
74_S	106_F	0.647	0.13
69_F	110_Q	0.640	0.13
36_A	139_L	0.639	0.13
83_L	134_F	0.637	0.13
81_L	107_V	0.636	0.13
97_G	104_W	0.636	0.13
62_S	107_V	0.629	0.12
101_V	147_N	0.626	0.12
70_L	131_F	0.626	0.12
114_D	118_F	0.619	0.12
95_D	174_K	0.615	0.12
54_R	106_F	0.614	0.12
67_A	71_G	0.613	0.12
100_F	119_G	0.611	0.12
152_L	167_D	0.609	0.12
156_D	167_D	0.609	0.12
122_L	129_T	0.604	0.12
56_Y	137_R	0.604	0.12
65_F	107_V	0.600	0.12
36_A	126_A	0.596	0.12
67_A	141_K	0.596	0.12
33_H	90_T	0.587	0.12
126_A	134_F	0.581	0.12
57_H	173_T	0.580	0.12
92_S	150_N	0.575	0.11
44_T	67_A	0.575	0.11
76_L	163_T	0.574	0.11
66_I	100_F	0.573	0.11
34_I	125_A	0.570	0.11
39_S	109_T	0.568	0.11
125_A	162_Q	0.559	0.11
99_S	103_L	0.557	0.11
38_A	108_L	0.550	0.11
112_R	154_A	0.548	0.11
81_L	89_I	0.547	0.11
117_P	121_A	0.544	0.11
96_F	121_A	0.542	0.11
138_Y	156_D	0.542	0.11
57_H	77_S	0.541	0.11
126_A	129_T	0.539	0.11
104_W	108_L	0.529	0.11
45_L	131_F	0.528	0.11
49_Y	86_T	0.527	0.11
64_M	158_T	0.524	0.11
32_K	99_S	0.516	0.11
89_I	130_V	0.514	0.11
64_M	163_T	0.514	0.11
77_S	80_M	0.513	0.10
132_E	136_H	0.513	0.10
40_K	136_H	0.513	0.10
94_A	174_K	0.512	0.10
79_D	132_E	0.506	0.10
40_K	79_D	0.506	0.10
103_L	124_S	0.503	0.10
102_I	131_F	0.500	0.10
58_A	120_A	0.500	0.10

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
1ciiA	1	0.486	36.6	0.952	Contact Map
3effK	4	0.7095	33.6	0.953	Contact Map
3pjsK	4	0.7095	30.4	0.954	Contact Map
4h33A	3	0.4693	19.6	0.958	Contact Map
1lnqA	6	0.581	18.3	0.959	Contact Map
4gx0A	3	0.743	7.5	0.965	Contact Map
4bgnA	3	0.6816	6.9	0.966	Contact Map
2qksA	4	0.8492	5.9	0.967	Contact Map
2i88A	1	0.4916	5.7	0.967	Contact Map
4ev6A	3	0.486	5.1	0.968	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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