YDIP - BACSU - GREMLIN Contacts

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YDIP - Probable BsuMI modification methylase subunit YdiP

UniProt:	O34680	Sequences: MKVVSLFSGIGGIELGLHQSGHTTEIFCEVDPLAKAVLSKNFPGVKIEDDINEIRELPSCDLVAAGFPCQDLSQAGGKEGIDGSRSGLVKKLFELIEKKEHANRPPWILIENVPYMLRLNRGKAMSYLTSVLSELGYTWAYRTVDARCFGLPQRRHRVILLASLFEDPKDVIFSQDHSEPDLDGKPSVVDHSNYYGFYWTEGLRGVGWAREAVPPIKCGSSVGIASPPAVWSPYEDIVGTINIRDAERLQGFPEDWTNITTETGKDIKEGARWRLVGNAVSVRVSKWIGENLSQPKGSISDFEGELVTKTWPSAAWGYGDKKYKVPVSKWVANTEQIAISEFLNHPLKPLSARALNGFLGRAARCTNVNYSDEFINSLERCKDRQLQKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	389 (301)
Sequences:	719 (573)
Seq/√Len:	33.0

ECOLI - DCM
BACSU - YDIP YDIO MTBP
SULSO - Q980M6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
248_R	254_E	7.057	1.00
17_L	289_G	6.850	1.00
108_I	162_A	5.906	1.00
5_S	14_E	5.231	1.00
65_A	92_L	4.452	1.00
114_P	156_H	4.034	1.00
91_K	94_E	3.965	1.00
8_S	29_E	3.908	1.00
19_Q	286_K	3.827	1.00
17_L	62_L	3.594	1.00
71_D	83_G	3.406	1.00
146_A	281_S	3.365	1.00
251_G	283_R	3.217	1.00
37_V	275_L	3.153	1.00
61_D	106_P	3.040	1.00
71_D	86_S	2.873	1.00
12_G	252_F	2.753	1.00
239_G	245_D	2.702	1.00
286_K	290_E	2.681	1.00
281_S	284_V	2.619	1.00
2_K	23_T	2.442	0.99
16_G	20_S	2.414	0.99
50_D	53_E	2.327	0.99
70_Q	85_R	2.299	0.99
7_F	280_V	2.133	0.99
246_A	273_W	2.111	0.98
96_I	108_I	2.099	0.98
6_L	63_V	2.052	0.98
5_S	8_S	2.021	0.98
241_I	246_A	2.008	0.98
105_P	137_Y	1.980	0.98
146_A	284_V	1.975	0.98
33_L	271_A	1.952	0.97
16_G	280_V	1.831	0.96
97_E	135_L	1.828	0.96
17_L	64_A	1.791	0.96
27_F	38_L	1.773	0.96
12_G	16_G	1.739	0.95
151_L	281_S	1.692	0.94
117_L	158_V	1.651	0.93
7_F	11_G	1.606	0.92
244_R	247_E	1.604	0.92
104_R	164_L	1.598	0.92
17_L	109_L	1.566	0.91
7_F	88_L	1.557	0.91
31_D	34_A	1.540	0.91
217_K	222_V	1.540	0.91
92_L	110_I	1.539	0.91
58_P	103_N	1.538	0.91
252_F	279_A	1.530	0.90
39_S	48_E	1.524	0.90
4_V	26_I	1.523	0.90
247_E	258_N	1.516	0.90
28_C	51_I	1.506	0.90
219_G	222_V	1.490	0.89
243_I	269_E	1.487	0.89
247_E	272_R	1.467	0.88
71_D	87_G	1.440	0.88
251_G	284_V	1.421	0.87
145_D	154_R	1.420	0.87
3_V	24_T	1.402	0.86
247_E	276_V	1.386	0.85
65_A	289_G	1.378	0.85
86_S	124_A	1.375	0.85
119_L	124_A	1.368	0.85
92_L	96_I	1.352	0.84
270_G	274_R	1.337	0.83
69_C	155_R	1.299	0.81
217_K	221_S	1.278	0.80
63_V	92_L	1.271	0.80
214_P	222_V	1.259	0.79
29_E	38_L	1.254	0.79
131_V	135_L	1.247	0.79
67_F	92_L	1.232	0.78
64_A	289_G	1.230	0.78
305_E	308_T	1.230	0.78
72_L	86_S	1.226	0.77
11_G	280_V	1.223	0.77
76_G	85_R	1.223	0.77
120_N	123_K	1.220	0.77
6_L	28_C	1.215	0.77
112_N	155_R	1.213	0.77
29_E	66_G	1.212	0.77
130_S	134_E	1.210	0.77
7_F	67_F	1.207	0.76
13_I	280_V	1.190	0.75
4_V	60_C	1.184	0.75
125_M	141_Y	1.183	0.75
79_E	82_D	1.182	0.75
66_G	250_Q	1.170	0.74
29_E	43_P	1.168	0.74
67_F	128_L	1.157	0.73
63_V	96_I	1.153	0.73
93_F	131_V	1.149	0.73
280_V	289_G	1.133	0.72
174_S	178_S	1.125	0.71
28_C	49_D	1.124	0.71
8_S	27_F	1.122	0.71
113_V	155_R	1.116	0.70
34_A	278_N	1.113	0.70
10_I	275_L	1.112	0.70
306_L	311_W	1.109	0.70
36_A	39_S	1.104	0.70
123_K	126_S	1.101	0.69
129_T	139_W	1.098	0.69
290_E	293_S	1.091	0.69
5_S	124_A	1.088	0.68
13_I	66_G	1.085	0.68
228_P	231_W	1.066	0.67
157_R	277_G	1.065	0.67
10_I	279_A	1.053	0.66
12_G	20_S	1.053	0.66
226_S	229_A	1.051	0.66
15_L	253_P	1.040	0.65
108_I	132_L	1.039	0.65
187_S	190_D	1.032	0.64
31_D	271_A	1.031	0.64
60_C	63_V	1.030	0.64
69_C	112_N	1.027	0.64
7_F	51_I	1.023	0.64
244_R	248_R	1.016	0.63
12_G	282_V	1.015	0.63
16_G	289_G	1.011	0.63
159_I	243_I	1.009	0.62
204_R	217_K	1.003	0.62
227_P	230_V	1.002	0.62
94_E	98_K	0.999	0.62
307_V	310_T	0.999	0.62
146_A	159_I	0.995	0.61
203_L	214_P	0.995	0.61
305_E	310_T	0.989	0.61
204_R	219_G	0.988	0.61
211_E	214_P	0.980	0.60
244_R	254_E	0.976	0.60
69_C	113_V	0.962	0.59
15_L	18_H	0.952	0.58
174_S	183_D	0.943	0.57
204_R	214_P	0.940	0.57
10_I	16_G	0.939	0.57
125_M	160_L	0.939	0.57
35_K	48_E	0.938	0.57
247_E	279_A	0.936	0.57
159_I	288_I	0.935	0.57
251_G	282_V	0.935	0.57
68_P	85_R	0.934	0.56
214_P	220_S	0.934	0.56
179_E	182_L	0.931	0.56
229_A	241_I	0.931	0.56
72_L	83_G	0.928	0.56
109_L	161_L	0.927	0.56
40_K	257_T	0.927	0.56
134_E	160_L	0.919	0.55
224_I	229_A	0.918	0.55
15_L	256_W	0.917	0.55
3_V	27_F	0.916	0.55
205_G	222_V	0.915	0.55
214_P	217_K	0.914	0.55
207_G	214_P	0.914	0.55
69_C	157_R	0.900	0.54
216_I	246_A	0.900	0.54
213_V	249_L	0.898	0.54
232_S	235_E	0.898	0.54
268_K	271_A	0.894	0.53
183_D	187_S	0.891	0.53
7_F	239_G	0.890	0.53
247_E	257_T	0.887	0.53
12_G	280_V	0.886	0.53
76_G	83_G	0.880	0.52
10_I	41_N	0.879	0.52
98_K	126_S	0.877	0.52
97_E	104_R	0.872	0.51
243_I	276_V	0.869	0.51
3_V	14_E	0.869	0.51
72_L	124_A	0.868	0.51
143_T	156_H	0.864	0.51
86_S	89_V	0.859	0.50
13_I	16_G	0.859	0.50
293_S	297_G	0.858	0.50
53_E	57_L	0.857	0.50
5_S	34_A	0.854	0.50
206_V	217_K	0.854	0.50
65_A	70_Q	0.852	0.50
70_Q	76_G	0.851	0.50
96_I	162_A	0.850	0.50
204_R	220_S	0.849	0.49
37_V	83_G	0.845	0.49
25_E	95_L	0.841	0.49
208_W	211_E	0.840	0.49
66_G	153_Q	0.834	0.48
24_T	38_L	0.833	0.48
59_S	103_N	0.828	0.48
17_L	20_S	0.828	0.48
10_I	258_N	0.826	0.48
71_D	124_A	0.824	0.47
14_E	24_T	0.823	0.47
303_E	308_T	0.823	0.47
8_S	124_A	0.821	0.47
240_T	273_W	0.820	0.47
14_E	27_F	0.819	0.47
72_L	256_W	0.818	0.47
205_G	219_G	0.818	0.47
301_D	307_V	0.816	0.47
14_E	38_L	0.815	0.47
33_L	216_I	0.812	0.46
77_G	108_I	0.811	0.46
13_I	285_S	0.810	0.46
93_F	279_A	0.805	0.46
146_A	151_L	0.801	0.45
225_A	230_V	0.799	0.45
65_A	85_R	0.798	0.45
41_N	287_W	0.798	0.45
178_S	182_L	0.797	0.45
290_E	294_Q	0.792	0.45
204_R	207_G	0.788	0.44
73_S	112_N	0.787	0.44
228_P	236_D	0.787	0.44
97_E	131_V	0.784	0.44
88_L	215_P	0.782	0.44
72_L	118_R	0.778	0.44
35_K	39_S	0.777	0.43
83_G	87_G	0.777	0.43
272_R	276_V	0.776	0.43
215_P	239_G	0.774	0.43
301_D	308_T	0.773	0.43
267_I	279_A	0.772	0.43
140_A	173_F	0.771	0.43
126_S	300_S	0.770	0.43
59_S	106_P	0.769	0.43
136_G	164_L	0.768	0.43
303_E	306_L	0.766	0.43
182_L	190_D	0.763	0.42
37_V	247_E	0.762	0.42
242_N	245_D	0.762	0.42
132_L	162_A	0.760	0.42
62_L	289_G	0.760	0.42
14_E	34_A	0.758	0.42
239_G	280_V	0.756	0.42
2_K	25_E	0.754	0.42
17_L	280_V	0.753	0.42
29_E	35_K	0.750	0.41
204_R	218_C	0.749	0.41
203_L	206_V	0.749	0.41
54_I	58_P	0.749	0.41
300_S	304_G	0.746	0.41
307_V	311_W	0.746	0.41
14_E	67_F	0.743	0.41
177_H	181_D	0.741	0.41
194_Y	197_F	0.741	0.41
75_A	273_W	0.740	0.40
187_S	191_H	0.738	0.40
23_T	44_G	0.733	0.40
207_G	232_S	0.732	0.40
117_L	141_Y	0.731	0.40
190_D	193_N	0.729	0.40
232_S	236_D	0.727	0.39
223_G	232_S	0.726	0.39
29_E	276_V	0.724	0.39
27_F	45_V	0.723	0.39
8_S	63_V	0.722	0.39
12_G	279_A	0.721	0.39
28_C	35_K	0.721	0.39
69_C	277_G	0.720	0.39
52_N	91_K	0.717	0.39
116_M	158_V	0.716	0.39
158_V	282_V	0.714	0.38
145_D	238_V	0.713	0.38
94_E	164_L	0.713	0.38
98_K	103_N	0.710	0.38
207_G	221_S	0.706	0.38
78_K	115_Y	0.705	0.38
140_A	149_F	0.700	0.37
41_N	257_T	0.697	0.37
303_E	309_K	0.697	0.37
39_S	97_E	0.695	0.37
189_V	193_N	0.693	0.37
123_K	127_Y	0.692	0.37
2_K	170_D	0.692	0.37
304_G	308_T	0.692	0.37
60_C	103_N	0.687	0.36
71_D	89_V	0.687	0.36
63_V	156_H	0.687	0.36
198_Y	201_E	0.686	0.36
8_S	64_A	0.686	0.36
67_F	280_V	0.682	0.36
128_L	160_L	0.682	0.36
10_I	282_V	0.678	0.36
226_S	230_V	0.676	0.35
20_S	286_K	0.674	0.35
55_R	84_S	0.673	0.35
19_Q	290_E	0.673	0.35
97_E	136_G	0.671	0.35
40_K	287_W	0.669	0.35
8_S	14_E	0.668	0.35
68_P	88_L	0.665	0.35
206_V	218_C	0.662	0.34
244_R	255_D	0.661	0.34
159_I	285_S	0.661	0.34
151_L	210_R	0.660	0.34
148_C	296_K	0.660	0.34
212_A	216_I	0.657	0.34
106_P	164_L	0.654	0.34
230_V	235_E	0.653	0.34
249_L	269_E	0.652	0.34
42_F	45_V	0.650	0.34
5_S	24_T	0.648	0.33
3_V	90_K	0.648	0.33
138_T	165_F	0.648	0.33
31_D	50_D	0.648	0.33
109_L	288_I	0.648	0.33
95_L	103_N	0.647	0.33
306_L	309_K	0.647	0.33
47_I	271_A	0.644	0.33
53_E	104_R	0.644	0.33
218_C	222_V	0.643	0.33
214_P	229_A	0.643	0.33
9_G	278_N	0.643	0.33
6_L	13_I	0.642	0.33
67_F	256_W	0.639	0.33
137_Y	164_L	0.639	0.33
32_P	255_D	0.638	0.33
24_T	45_V	0.637	0.33
51_I	60_C	0.635	0.32
224_I	231_W	0.635	0.32
66_G	248_R	0.632	0.32
26_I	47_I	0.631	0.32
196_G	202_G	0.631	0.32
224_I	232_S	0.630	0.32
228_P	233_P	0.630	0.32
89_V	128_L	0.627	0.32
303_E	311_W	0.626	0.32
71_D	238_V	0.620	0.31
67_F	116_M	0.619	0.31
62_L	109_L	0.618	0.31
306_L	310_T	0.616	0.31
18_H	110_I	0.614	0.31
83_G	275_L	0.608	0.30
74_Q	116_M	0.607	0.30
250_Q	280_V	0.607	0.30
206_V	232_S	0.604	0.30
3_V	64_A	0.604	0.30
161_L	292_L	0.604	0.30
43_P	94_E	0.603	0.30
55_R	58_P	0.602	0.30
225_A	229_A	0.602	0.30
155_R	277_G	0.600	0.30
148_C	174_S	0.600	0.30
4_V	41_N	0.599	0.30
207_G	219_G	0.599	0.30
70_Q	81_I	0.598	0.30
257_T	272_R	0.596	0.30
23_T	293_S	0.595	0.30
128_L	141_Y	0.594	0.29
84_S	87_G	0.592	0.29
106_P	167_D	0.592	0.29
74_Q	115_Y	0.591	0.29
228_P	232_S	0.590	0.29
182_L	188_V	0.590	0.29
131_V	134_E	0.589	0.29
304_G	309_K	0.589	0.29
56_E	126_S	0.588	0.29
230_V	270_G	0.587	0.29
204_R	222_V	0.584	0.29
49_D	53_E	0.584	0.29
107_W	138_T	0.578	0.28
232_S	237_I	0.577	0.28
227_P	232_S	0.576	0.28
134_E	190_D	0.571	0.28
66_G	112_N	0.569	0.28
6_L	95_L	0.568	0.28
147_R	247_E	0.568	0.28
294_Q	302_F	0.567	0.28
29_E	124_A	0.566	0.28
11_G	17_L	0.566	0.28
179_E	190_D	0.565	0.28
12_G	250_Q	0.565	0.28
244_R	256_W	0.561	0.27
12_G	67_F	0.560	0.27
13_I	284_V	0.560	0.27
13_I	242_N	0.560	0.27
138_T	170_D	0.560	0.27
18_H	44_G	0.559	0.27
153_Q	250_Q	0.556	0.27
72_L	153_Q	0.556	0.27
151_L	251_G	0.555	0.27
252_F	258_N	0.555	0.27
17_L	29_E	0.554	0.27
8_S	12_G	0.552	0.27
208_W	219_G	0.552	0.27
41_N	258_N	0.550	0.27
271_A	279_A	0.550	0.27
303_E	310_T	0.549	0.26
212_A	260_T	0.547	0.26
28_C	48_E	0.544	0.26
28_C	95_L	0.544	0.26
207_G	220_S	0.544	0.26
6_L	92_L	0.543	0.26
203_L	221_S	0.542	0.26
153_Q	278_N	0.541	0.26
11_G	16_G	0.541	0.26
243_I	285_S	0.540	0.26
176_D	310_T	0.540	0.26
205_G	213_V	0.540	0.26
13_I	159_I	0.537	0.26
26_I	103_N	0.537	0.26
90_K	124_A	0.536	0.26
44_G	255_D	0.536	0.26
14_E	92_L	0.535	0.26
178_S	190_D	0.534	0.25
67_F	120_N	0.534	0.25
12_G	34_A	0.531	0.25
76_G	95_L	0.531	0.25
2_K	176_D	0.531	0.25
115_Y	273_W	0.530	0.25
125_M	256_W	0.530	0.25
133_S	138_T	0.530	0.25
305_E	311_W	0.529	0.25
298_S	302_F	0.527	0.25
218_C	242_N	0.527	0.25
60_C	104_R	0.525	0.25
181_D	185_K	0.525	0.25
31_D	91_K	0.524	0.25
26_I	57_L	0.523	0.25
185_K	190_D	0.522	0.25
11_G	38_L	0.520	0.25
6_L	66_G	0.519	0.25
116_M	128_L	0.519	0.25
10_I	281_S	0.519	0.25
152_P	176_D	0.518	0.25
7_F	13_I	0.518	0.25
150_G	214_P	0.517	0.24
184_G	187_S	0.517	0.24
227_P	233_P	0.515	0.24
28_C	118_R	0.515	0.24
149_F	284_V	0.514	0.24
203_L	279_A	0.514	0.24
140_A	172_I	0.514	0.24
25_E	93_F	0.513	0.24
204_R	221_S	0.513	0.24
132_L	139_W	0.512	0.24
193_N	254_E	0.512	0.24
112_N	157_R	0.510	0.24
225_A	231_W	0.510	0.24
8_S	11_G	0.508	0.24
88_L	91_K	0.508	0.24
39_S	43_P	0.506	0.24
6_L	289_G	0.504	0.24
38_L	289_G	0.502	0.24
298_S	309_K	0.501	0.23
10_I	37_V	0.500	0.23
7_F	24_T	0.500	0.23
11_G	88_L	0.500	0.23
59_S	304_G	0.500	0.23

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
3swrA	1	0.7326	100	0.282	Contact Map
4ft4B	1	0.7635	100	0.303	Contact Map
4wxxA	1	0.7455	100	0.308	Contact Map
4dkjA	1	0.7326	100	0.313	Contact Map
2c7pA	1	0.7378	100	0.316	Contact Map
3g7uA	1	0.6761	100	0.347	Contact Map
3ubtY	2	0.7429	100	0.35	Contact Map
3qv2A	1	0.7018	100	0.351	Contact Map
3me5A	1	0.7352	100	0.357	Contact Map
4h0nA	1	0.7147	100	0.359	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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