YORM - BACSU - GREMLIN Contacts

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YORM - SPBc2 prophage-derived uncharacterized protein YorM

UniProt:	O31901	Sequences: MFKKLIDKHKKYVYHRINKMALFATIGLLGVGLVYSAKNLYTHQDNQVSIKKSFYLNKKEVRQKLIHEIDVPRILPRLKSEEEKQAESRKKYLNATITYLTEENKKAAKHTKTKKVQKTNTKRNLDKAVSKSTNAKAVKSHEVVATAYTAFCSTGCTGKTRTGYDVSNTSYYNGKRIIAVDPEVIPLYSLVQVSYEGNSFQAYAIDTGGDIKNNRIDILMDSEQEANAFGRKNVRVSW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	238 (219)
Sequences:	804 (726)
Seq/√Len:	49.0

BACSU - YORM YABE YOCH YUIC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
164_Y	205_I	4.852	1.00
144_V	231_R	4.555	1.00
178_I	191_V	4.244	1.00
222_S	225_E	3.743	1.00
143_V	236_V	2.841	1.00
106_K	109_K	2.729	1.00
152_C	156_C	2.717	1.00
192_Q	237_S	2.656	1.00
144_V	215_R	2.643	1.00
143_V	178_I	2.631	1.00
196_E	202_A	2.503	1.00
140_S	237_S	2.264	1.00
142_E	235_R	2.092	1.00
180_V	204_A	2.088	1.00
166_V	219_L	2.078	1.00
145_A	229_F	2.033	1.00
150_A	166_V	2.026	1.00
194_S	235_R	1.978	0.99
164_Y	177_I	1.920	0.99
161_R	207_T	1.914	0.99
167_S	177_I	1.903	0.99
196_E	218_I	1.880	0.99
161_R	187_L	1.860	0.99
149_T	223_E	1.808	0.99
187_L	207_T	1.783	0.99
86_A	124_N	1.781	0.99
223_E	227_N	1.762	0.99
93_L	114_K	1.749	0.99
210_D	215_R	1.734	0.99
152_C	158_G	1.729	0.99
151_F	219_L	1.706	0.98
147_A	229_F	1.691	0.98
150_A	219_L	1.656	0.98
177_I	219_L	1.652	0.98
218_I	229_F	1.584	0.97
78_L	81_E	1.575	0.97
204_A	207_T	1.566	0.97
70_D	122_K	1.558	0.97
229_F	234_V	1.531	0.97
149_T	152_C	1.508	0.96
99_Y	109_K	1.491	0.96
88_S	91_K	1.486	0.96
145_A	220_M	1.485	0.96
137_A	237_S	1.482	0.96
218_I	232_K	1.470	0.96
33_L	102_E	1.469	0.96
147_A	220_M	1.467	0.96
229_F	232_K	1.457	0.96
152_C	157_T	1.443	0.95
150_A	158_G	1.441	0.95
55_Y	98_T	1.439	0.95
64_K	90_K	1.413	0.95
220_M	226_A	1.405	0.95
182_P	185_I	1.365	0.94
99_Y	106_K	1.362	0.94
184_V	214_N	1.348	0.93
151_F	167_S	1.348	0.93
150_A	155_G	1.339	0.93
177_I	205_I	1.335	0.93
14_Y	24_A	1.314	0.93
84_K	88_S	1.307	0.92
202_A	234_V	1.302	0.92
164_Y	203_Y	1.300	0.92
89_R	118_K	1.295	0.92
98_T	110_H	1.287	0.92
138_V	237_S	1.282	0.92
196_E	234_V	1.275	0.91
143_V	234_V	1.274	0.91
168_N	176_R	1.270	0.91
140_S	235_R	1.268	0.91
145_A	234_V	1.265	0.91
143_V	229_F	1.260	0.91
167_S	219_L	1.254	0.91
149_T	156_C	1.252	0.91
144_V	233_N	1.247	0.90
152_C	155_G	1.235	0.90
169_T	176_R	1.209	0.89
211_I	215_R	1.208	0.89
215_R	231_R	1.206	0.89
185_I	204_A	1.205	0.89
168_N	225_E	1.188	0.88
140_S	143_V	1.178	0.88
190_L	201_Q	1.167	0.87
21_A	32_G	1.161	0.87
209_G	231_R	1.157	0.87
34_V	38_K	1.149	0.86
143_V	218_I	1.144	0.86
32_G	52_K	1.139	0.86
176_R	221_D	1.134	0.86
165_D	169_T	1.134	0.86
180_V	207_T	1.127	0.85
180_V	185_I	1.123	0.85
185_I	216_I	1.116	0.85
164_Y	167_S	1.114	0.85
178_I	216_I	1.102	0.84
26_I	50_I	1.096	0.84
190_L	203_Y	1.092	0.83
145_A	216_I	1.091	0.83
145_A	196_E	1.088	0.83
161_R	209_G	1.084	0.83
149_T	158_G	1.061	0.82
152_C	219_L	1.058	0.81
202_A	218_I	1.058	0.81
224_Q	228_A	1.057	0.81
77_R	80_S	1.049	0.81
195_Y	229_F	1.030	0.80
14_Y	19_K	1.029	0.80
181_D	211_I	1.024	0.79
94_N	115_K	1.023	0.79
20_M	24_A	1.019	0.79
193_V	221_D	1.014	0.79
156_C	226_A	1.006	0.78
167_S	176_R	1.005	0.78
34_V	50_I	1.000	0.78
74_I	77_R	0.987	0.77
28_L	52_K	0.986	0.77
145_A	202_A	0.985	0.77
158_G	166_V	0.982	0.76
183_E	212_K	0.982	0.76
152_C	166_V	0.981	0.76
169_T	203_Y	0.972	0.76
97_I	111_T	0.971	0.76
15_H	20_M	0.968	0.75
178_I	236_V	0.968	0.75
182_P	204_A	0.966	0.75
223_E	226_A	0.966	0.75
194_S	202_A	0.965	0.75
14_Y	23_F	0.950	0.74
87_E	123_R	0.950	0.74
14_Y	18_N	0.947	0.74
165_D	177_I	0.933	0.73
151_F	158_G	0.921	0.72
94_N	101_T	0.921	0.72
143_V	202_A	0.920	0.71
142_E	233_N	0.912	0.71
166_V	169_T	0.912	0.71
190_L	202_A	0.905	0.70
154_T	223_E	0.905	0.70
74_I	80_S	0.902	0.70
184_V	204_A	0.902	0.70
75_L	78_L	0.901	0.70
92_Y	118_K	0.899	0.70
187_L	204_A	0.896	0.69
95_A	111_T	0.896	0.69
149_T	155_G	0.894	0.69
12_Y	189_S	0.891	0.69
181_D	184_V	0.890	0.69
162_T	187_L	0.889	0.69
166_V	177_I	0.880	0.68
145_A	215_R	0.876	0.68
91_K	103_E	0.873	0.67
75_L	81_E	0.868	0.67
160_T	226_A	0.867	0.67
152_C	223_E	0.863	0.67
211_I	214_N	0.863	0.67
85_Q	88_S	0.862	0.66
120_N	123_R	0.861	0.66
178_I	218_I	0.859	0.66
180_V	184_V	0.852	0.66
197_G	207_T	0.852	0.66
132_S	137_A	0.847	0.65
14_Y	20_M	0.841	0.65
193_V	237_S	0.840	0.64
21_A	28_L	0.835	0.64
119_T	218_I	0.834	0.64
67_H	91_K	0.833	0.64
193_V	229_F	0.831	0.64
67_H	88_S	0.829	0.63
145_A	189_S	0.824	0.63
97_I	109_K	0.813	0.62
165_D	237_S	0.807	0.61
91_K	104_N	0.800	0.61
82_E	85_Q	0.798	0.60
9_H	25_T	0.788	0.59
53_S	103_E	0.787	0.59
155_G	159_K	0.772	0.58
96_T	113_T	0.772	0.58
150_A	156_C	0.769	0.58
166_V	205_I	0.766	0.57
220_M	229_F	0.759	0.57
155_G	158_G	0.757	0.56
132_S	135_A	0.750	0.56
193_V	234_V	0.749	0.56
166_V	193_V	0.745	0.55
194_S	234_V	0.744	0.55
184_V	213_N	0.744	0.55
143_V	196_E	0.741	0.55
11_K	20_M	0.741	0.55
181_D	212_K	0.739	0.55
80_S	91_K	0.735	0.54
193_V	196_E	0.735	0.54
67_H	73_R	0.733	0.54
196_E	205_I	0.732	0.54
205_I	219_L	0.728	0.53
166_V	221_D	0.724	0.53
192_Q	201_Q	0.722	0.53
32_G	53_S	0.718	0.52
180_V	187_L	0.718	0.52
80_S	88_S	0.717	0.52
152_C	226_A	0.717	0.52
192_Q	205_I	0.715	0.52
165_D	221_D	0.713	0.52
181_D	187_L	0.710	0.52
128_A	132_S	0.709	0.52
151_F	223_E	0.706	0.51
194_S	201_Q	0.706	0.51
162_T	205_I	0.704	0.51
181_D	213_N	0.699	0.51
84_K	91_K	0.696	0.50
162_T	188_Y	0.696	0.50
193_V	202_A	0.694	0.50
18_N	22_L	0.689	0.50
201_Q	212_K	0.689	0.50
55_Y	58_K	0.688	0.49
160_T	166_V	0.688	0.49
176_R	196_E	0.687	0.49
143_V	187_L	0.682	0.49
145_A	218_I	0.680	0.49
143_V	232_K	0.674	0.48
208_G	217_D	0.673	0.48
184_V	187_L	0.671	0.48
101_T	106_K	0.670	0.48
115_K	119_T	0.670	0.48
63_Q	67_H	0.663	0.47
15_H	42_T	0.660	0.47
181_D	204_A	0.659	0.46
202_A	207_T	0.658	0.46
189_S	205_I	0.657	0.46
31_V	35_Y	0.655	0.46
193_V	216_I	0.655	0.46
169_T	237_S	0.653	0.46
14_Y	17_I	0.647	0.45
21_A	26_I	0.646	0.45
189_S	203_Y	0.646	0.45
69_I	88_S	0.644	0.45
165_D	205_I	0.644	0.45
66_I	74_I	0.641	0.45
224_Q	227_N	0.641	0.45
150_A	176_R	0.639	0.44
147_A	226_A	0.630	0.44
32_G	36_S	0.628	0.43
88_S	104_N	0.627	0.43
100_L	108_A	0.625	0.43
10_K	40_L	0.625	0.43
51_K	103_E	0.624	0.43
180_V	196_E	0.621	0.43
143_V	194_S	0.619	0.42
151_F	154_T	0.617	0.42
23_F	29_L	0.616	0.42
13_V	17_I	0.613	0.42
196_E	204_A	0.611	0.42
73_R	79_K	0.607	0.41
116_V	119_T	0.601	0.41
35_Y	177_I	0.599	0.40
72_P	83_E	0.598	0.40
102_E	107_A	0.597	0.40
184_V	210_D	0.596	0.40
221_D	225_E	0.593	0.40
149_T	154_T	0.588	0.39
132_S	136_K	0.588	0.39
112_K	116_V	0.586	0.39
159_K	215_R	0.586	0.39
197_G	218_I	0.583	0.39
72_P	75_L	0.583	0.39
36_S	48_V	0.580	0.39
182_P	207_T	0.580	0.39
32_G	38_K	0.577	0.38
151_F	156_C	0.577	0.38
17_I	21_A	0.577	0.38
68_E	79_K	0.575	0.38
165_D	168_N	0.574	0.38
147_A	232_K	0.572	0.38
187_L	191_V	0.571	0.38
116_V	233_N	0.570	0.38
194_S	197_G	0.569	0.38
187_L	193_V	0.568	0.38
94_N	120_N	0.567	0.37
176_R	205_I	0.563	0.37
143_V	189_S	0.560	0.37
226_A	232_K	0.560	0.37
12_Y	15_H	0.558	0.37
192_Q	197_G	0.558	0.37
176_R	237_S	0.554	0.36
29_L	54_F	0.553	0.36
120_N	124_N	0.552	0.36
152_C	176_R	0.549	0.36
219_L	223_E	0.547	0.36
158_G	177_I	0.547	0.36
69_I	84_K	0.546	0.35
169_T	193_V	0.543	0.35
21_A	24_A	0.540	0.35
44_Q	64_K	0.539	0.35
135_A	237_S	0.538	0.35
15_H	27_G	0.538	0.35
151_F	155_G	0.537	0.35
113_T	116_V	0.536	0.35
16_R	19_K	0.530	0.34
165_D	176_R	0.529	0.34
133_T	136_K	0.529	0.34
193_V	235_R	0.526	0.34
108_A	218_I	0.526	0.34
181_D	216_I	0.526	0.34
15_H	23_F	0.525	0.34
30_G	40_L	0.525	0.34
187_L	211_I	0.524	0.33
142_E	232_K	0.523	0.33
16_R	26_I	0.523	0.33
154_T	158_G	0.522	0.33
67_H	104_N	0.521	0.33
88_S	93_L	0.520	0.33
168_N	221_D	0.519	0.33
70_D	94_N	0.518	0.33
196_E	229_F	0.517	0.33
155_G	166_V	0.515	0.33
21_A	38_K	0.514	0.33
63_Q	74_I	0.513	0.32
184_V	236_V	0.512	0.32
121_T	124_N	0.510	0.32
116_V	125_L	0.510	0.32
13_V	23_F	0.508	0.32
115_K	122_K	0.507	0.32
191_V	202_A	0.507	0.32
217_D	230_G	0.507	0.32
149_T	157_T	0.506	0.32
49_S	57_N	0.505	0.32
101_T	109_K	0.504	0.32
184_V	207_T	0.502	0.31
48_V	84_K	0.500	0.31

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
4wjtA	2	0.437	100	0.484	Contact Map
2ae0X	1	0.7437	99.9	0.646	Contact Map
2g5dA	1	0.7269	99.9	0.662	Contact Map
2pnwA	1	0.7521	99.9	0.669	Contact Map
3czbA	2	0.7227	99.8	0.684	Contact Map
4fuoA	2	0.542	97.2	0.883	Contact Map
4avrA	2	0.3739	96.8	0.89	Contact Map
3eo5A	1	0.6891	96.6	0.892	Contact Map
4fzqA	4	0.3319	95.6	0.901	Contact Map
2ltjA	1	0.4664	95.5	0.902	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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