YKTD - BACSU - GREMLIN Contacts

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YKTD - Putative S-adenosyl-L-methionine-dependent methyltransferase YktD

UniProt:	Q45500	Sequences: MRKNESSLTSLISAFARAYHSRYDTPLIFDDFIAKDLINEKEFIDISKNMIQEISFFNKEIAERLQNDPEKILKWVAQIQLSPTPLARASYCEKVLHNELILGAKQYVILGAGLDTFCFRHPELENSLQVFEVDHPATQQLKKNKLKDANLTIPGHLHFVPMDFTKTFSYDPLLDEGFKNTKTFFSLLGVSYYVTREENASLISNLFSHVPPGSSIVFDYADETLFTAKGTSNRVEHMVKMAAASGEPMKSCFTYQEIEHLLESSGLLIYEHLSPDDINDLFFSNRKDNLSAFETIHYIHAVKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	304 (258)
Sequences:	1945 (1433)
Seq/√Len:	89.2

BACSU - YKTD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_E	117_F	5.100	1.00
90_S	94_K	4.250	1.00
129_Q	158_H	4.144	1.00
22_R	35_K	3.796	1.00
108_V	185_F	3.768	1.00
96_L	184_F	3.629	1.00
171_D	175_D	3.102	1.00
195_T	198_E	2.673	1.00
183_T	210_V	2.541	1.00
178_F	183_T	2.474	1.00
21_S	30_D	2.470	1.00
187_L	202_L	2.463	1.00
93_E	120_R	2.454	1.00
185_F	210_V	2.431	1.00
274_S	277_D	2.332	1.00
132_E	142_K	2.253	1.00
273_L	281_L	2.155	1.00
107_Y	186_S	2.100	1.00
168_F	171_D	2.063	1.00
117_F	188_L	2.061	1.00
111_G	190_V	2.054	1.00
136_P	161_P	2.051	1.00
251_S	255_Y	2.044	1.00
131_F	177_G	2.015	1.00
143_K	159_F	1.996	1.00
139_Q	159_F	1.949	1.00
133_V	162_M	1.923	1.00
108_V	178_F	1.899	1.00
287_K	290_L	1.880	1.00
26_P	30_D	1.854	1.00
133_V	160_V	1.831	1.00
129_Q	156_H	1.819	1.00
37_L	145_K	1.787	1.00
44_I	47_S	1.756	1.00
200_A	265_S	1.725	1.00
92_C	188_L	1.712	1.00
185_F	206_L	1.681	1.00
276_D	282_F	1.679	1.00
89_A	117_F	1.662	1.00
261_L	265_S	1.651	1.00
112_A	132_E	1.643	1.00
131_F	160_V	1.616	1.00
257_E	260_H	1.614	1.00
174_L	180_N	1.607	1.00
260_H	264_S	1.605	1.00
7_S	10_S	1.562	1.00
98_N	101_I	1.547	1.00
277_D	282_F	1.545	1.00
223_E	252_C	1.542	1.00
20_H	23_Y	1.539	1.00
23_Y	26_P	1.514	1.00
167_T	172_P	1.508	1.00
21_S	29_F	1.505	1.00
247_E	252_C	1.502	1.00
35_K	39_N	1.491	1.00
239_V	243_A	1.478	1.00
139_Q	161_P	1.464	0.99
242_A	245_S	1.448	0.99
283_F	287_K	1.435	0.99
199_N	251_S	1.420	0.99
201_S	204_S	1.413	0.99
198_E	202_L	1.411	0.99
96_L	128_L	1.405	0.99
190_V	202_L	1.403	0.99
241_M	245_S	1.393	0.99
164_F	202_L	1.384	0.99
187_L	190_V	1.366	0.99
240_K	244_A	1.345	0.99
14_A	17_R	1.340	0.99
117_F	121_H	1.319	0.99
278_I	282_F	1.313	0.99
20_H	188_L	1.312	0.99
285_N	288_D	1.311	0.99
122_P	154_P	1.309	0.99
256_Q	261_L	1.306	0.99
7_S	135_H	1.305	0.99
139_Q	143_K	1.304	0.99
140_Q	144_N	1.297	0.99
144_N	148_D	1.279	0.99
119_F	157_L	1.271	0.99
164_F	190_V	1.263	0.98
133_V	169_S	1.261	0.98
170_Y	174_L	1.257	0.98
89_A	186_S	1.251	0.98
178_F	210_V	1.231	0.98
84_T	219_D	1.224	0.98
88_R	193_Y	1.213	0.98
173_L	178_F	1.202	0.98
99_E	184_F	1.202	0.98
238_M	242_A	1.199	0.98
170_Y	205_N	1.191	0.98
275_P	279_N	1.190	0.98
215_S	262_L	1.188	0.98
121_H	188_L	1.184	0.98
106_Q	132_E	1.178	0.98
284_S	287_K	1.175	0.98
108_V	131_F	1.172	0.97
89_A	188_L	1.167	0.97
7_S	138_T	1.166	0.97
21_S	32_F	1.164	0.97
9_T	13_S	1.151	0.97
277_D	283_F	1.144	0.97
100_L	107_Y	1.136	0.97
131_F	178_F	1.135	0.97
13_S	16_A	1.134	0.97
235_V	239_V	1.125	0.97
108_V	177_G	1.125	0.97
169_S	187_L	1.116	0.97
12_I	16_A	1.111	0.97
98_N	215_S	1.106	0.96
106_Q	131_F	1.103	0.96
121_H	267_L	1.101	0.96
84_T	238_M	1.096	0.96
12_I	192_Y	1.093	0.96
114_L	141_L	1.090	0.96
279_N	282_F	1.084	0.96
44_I	49_N	1.083	0.96
223_E	248_P	1.049	0.95
250_K	255_Y	1.030	0.95
169_S	214_S	1.029	0.95
109_I	132_E	1.025	0.95
117_F	130_V	1.018	0.94
277_D	281_L	1.018	0.94
92_C	186_S	1.016	0.94
206_L	216_I	1.016	0.94
96_L	186_S	1.008	0.94
29_F	86_L	1.008	0.94
234_R	237_H	1.004	0.94
276_D	280_D	1.002	0.94
238_M	241_M	1.001	0.94
11_L	15_F	1.000	0.94
106_Q	183_T	0.994	0.94
105_K	183_T	0.989	0.93
16_A	19_Y	0.988	0.93
165_T	198_E	0.983	0.93
77_A	81_L	0.980	0.93
271_E	281_L	0.978	0.93
172_P	195_T	0.975	0.93
228_A	234_R	0.969	0.93
283_F	290_L	0.969	0.93
78_Q	192_Y	0.967	0.93
143_K	147_K	0.967	0.93
81_L	238_M	0.966	0.93
236_E	240_K	0.964	0.93
106_Q	182_K	0.959	0.92
36_D	39_N	0.959	0.92
12_I	82_S	0.958	0.92
96_L	107_Y	0.952	0.92
95_V	184_F	0.951	0.92
273_L	277_D	0.951	0.92
47_S	50_M	0.951	0.92
11_L	38_I	0.949	0.92
24_D	33_I	0.940	0.92
11_L	219_D	0.938	0.91
83_P	86_L	0.937	0.91
37_L	112_A	0.934	0.91
249_M	252_C	0.929	0.91
107_Y	128_L	0.918	0.91
187_L	191_S	0.901	0.90
40_E	44_I	0.899	0.90
111_G	202_L	0.896	0.89
124_L	127_S	0.893	0.89
279_N	283_F	0.892	0.89
141_L	145_K	0.891	0.89
248_P	252_C	0.889	0.89
234_R	238_M	0.882	0.89
136_P	162_M	0.878	0.89
41_K	48_K	0.877	0.88
106_Q	178_F	0.876	0.88
258_I	261_L	0.875	0.88
174_L	208_S	0.874	0.88
247_E	250_K	0.872	0.88
7_S	29_F	0.871	0.88
172_P	204_S	0.869	0.88
38_I	42_E	0.867	0.88
109_I	130_V	0.867	0.88
223_E	226_F	0.862	0.88
36_D	149_A	0.856	0.87
135_H	138_T	0.854	0.87
197_E	201_S	0.849	0.87
29_F	47_S	0.847	0.87
174_L	209_H	0.845	0.87
182_K	211_P	0.844	0.86
17_R	89_A	0.836	0.86
191_S	202_L	0.834	0.86
11_L	43_F	0.833	0.86
80_Q	87_A	0.830	0.86
40_E	141_L	0.829	0.86
221_A	226_F	0.821	0.85
192_Y	221_A	0.821	0.85
279_N	284_S	0.815	0.85
204_S	208_S	0.814	0.84
234_R	241_M	0.812	0.84
158_H	161_P	0.808	0.84
276_D	284_S	0.804	0.84
107_Y	130_V	0.803	0.84
203_I	262_L	0.798	0.83
196_R	257_E	0.796	0.83
92_C	117_F	0.796	0.83
30_D	122_P	0.796	0.83
89_A	121_H	0.795	0.83
146_L	151_L	0.787	0.82
33_I	36_D	0.785	0.82
107_Y	184_F	0.778	0.82
162_M	172_P	0.772	0.81
99_E	103_G	0.772	0.81
204_S	265_S	0.771	0.81
240_K	243_A	0.771	0.81
50_M	203_I	0.770	0.81
152_T	264_S	0.765	0.81
37_L	141_L	0.763	0.80
167_T	173_L	0.752	0.79
243_A	246_G	0.750	0.79
201_S	205_N	0.744	0.79
19_Y	186_S	0.740	0.78
189_G	193_Y	0.739	0.78
251_S	261_L	0.737	0.78
112_A	142_K	0.733	0.78
10_S	14_A	0.733	0.78
81_L	112_A	0.723	0.77
20_H	117_F	0.723	0.77
172_P	175_D	0.721	0.77
20_H	28_I	0.720	0.76
96_L	130_V	0.718	0.76
16_A	86_L	0.717	0.76
89_A	93_E	0.716	0.76
283_F	286_R	0.715	0.76
175_D	197_E	0.713	0.76
108_V	173_L	0.713	0.76
206_L	210_V	0.712	0.76
95_V	215_S	0.706	0.75
99_E	119_F	0.705	0.75
24_D	235_V	0.704	0.75
16_A	238_M	0.703	0.75
23_Y	29_F	0.701	0.75
80_Q	192_Y	0.701	0.75
242_A	249_M	0.695	0.74
286_R	289_N	0.694	0.74
169_S	213_G	0.694	0.74
235_V	242_A	0.692	0.74
271_E	274_S	0.691	0.73
105_K	182_K	0.688	0.73
10_S	142_K	0.687	0.73
76_V	80_Q	0.685	0.73
33_I	37_L	0.685	0.73
15_F	18_A	0.682	0.72
249_M	255_Y	0.676	0.72
25_T	32_F	0.672	0.71
210_V	214_S	0.672	0.71
33_I	116_T	0.669	0.71
100_L	105_K	0.669	0.71
23_Y	82_S	0.668	0.71
227_T	234_R	0.663	0.70
260_H	263_E	0.661	0.70
281_L	288_D	0.661	0.70
273_L	283_F	0.661	0.70
165_T	195_T	0.661	0.70
206_L	209_H	0.659	0.70
21_S	25_T	0.659	0.70
280_D	284_S	0.658	0.70
84_T	192_Y	0.656	0.70
281_L	284_S	0.654	0.69
144_N	180_N	0.654	0.69
97_H	101_I	0.651	0.69
134_D	193_Y	0.651	0.69
94_K	98_N	0.649	0.69
229_K	240_K	0.649	0.69
118_C	130_V	0.647	0.69
93_E	188_L	0.646	0.68
88_R	189_G	0.641	0.68
239_V	252_C	0.640	0.68
19_Y	82_S	0.639	0.68
180_N	281_L	0.637	0.67
177_G	214_S	0.637	0.67
16_A	219_D	0.637	0.67
12_I	15_F	0.635	0.67
235_V	241_M	0.634	0.67
17_R	189_G	0.633	0.67
16_A	82_S	0.632	0.67
259_E	272_H	0.632	0.67
175_D	204_S	0.632	0.67
20_H	93_E	0.630	0.66
20_H	25_T	0.629	0.66
225_L	252_C	0.628	0.66
256_Q	280_D	0.628	0.66
135_H	139_Q	0.627	0.66
106_Q	177_G	0.623	0.66
164_F	262_L	0.622	0.65
164_F	209_H	0.622	0.65
277_D	280_D	0.621	0.65
160_V	262_L	0.618	0.65
7_S	16_A	0.618	0.65
84_T	234_R	0.618	0.65
251_S	254_T	0.617	0.65
226_F	229_K	0.617	0.65
160_V	206_L	0.614	0.64
137_A	140_Q	0.613	0.64
41_K	45_D	0.613	0.64
106_Q	109_I	0.612	0.64
107_Y	286_R	0.612	0.64
228_A	238_M	0.610	0.64
98_N	102_L	0.609	0.64
273_L	282_F	0.605	0.63
127_S	156_H	0.605	0.63
84_T	87_A	0.601	0.63
235_V	238_M	0.600	0.63
11_L	261_L	0.600	0.63
281_L	289_N	0.599	0.63
84_T	220_Y	0.599	0.63
97_H	100_L	0.596	0.62
277_D	284_S	0.596	0.62
283_F	288_D	0.587	0.61
13_S	192_Y	0.585	0.61
113_G	134_D	0.585	0.61
196_R	261_L	0.582	0.60
153_I	179_K	0.580	0.60
250_K	254_T	0.580	0.60
81_L	192_Y	0.579	0.60
22_R	32_F	0.578	0.60
13_S	85_P	0.577	0.60
169_S	172_P	0.576	0.60
204_S	207_F	0.576	0.60
200_A	254_T	0.575	0.59
111_G	205_N	0.575	0.59
191_S	199_N	0.572	0.59
19_Y	22_R	0.569	0.59
192_Y	219_D	0.568	0.59
259_E	263_E	0.568	0.59
91_Y	214_S	0.567	0.58
259_E	276_D	0.567	0.58
200_A	261_L	0.564	0.58
220_Y	272_H	0.564	0.58
187_L	203_I	0.562	0.58
11_L	41_K	0.556	0.57
276_D	279_N	0.555	0.57
32_F	51_I	0.553	0.57
12_I	85_P	0.551	0.56
145_K	149_A	0.548	0.56
6_S	9_T	0.547	0.56
142_K	146_L	0.541	0.55
189_G	220_Y	0.540	0.55
229_K	238_M	0.540	0.55
31_D	34_A	0.539	0.55
144_N	158_H	0.539	0.55
136_P	140_Q	0.538	0.54
211_P	214_S	0.536	0.54
216_I	269_I	0.536	0.54
49_N	52_Q	0.534	0.54
106_Q	214_S	0.534	0.54
77_A	242_A	0.533	0.54
109_I	226_F	0.532	0.54
187_L	219_D	0.530	0.53
252_C	255_Y	0.530	0.53
115_D	173_L	0.529	0.53
81_L	85_P	0.528	0.53
149_A	186_S	0.528	0.53
228_A	235_V	0.525	0.53
44_I	48_K	0.524	0.53
192_Y	251_S	0.524	0.53
89_A	92_C	0.522	0.52
147_K	153_I	0.522	0.52
187_L	199_N	0.522	0.52
285_N	289_N	0.521	0.52
276_D	281_L	0.521	0.52
171_D	176_E	0.519	0.52
39_N	261_L	0.518	0.52
136_P	264_S	0.516	0.51
199_N	261_L	0.514	0.51
160_V	172_P	0.513	0.51
89_A	120_R	0.513	0.51
129_Q	177_G	0.513	0.51
38_I	41_K	0.512	0.51
80_Q	235_V	0.512	0.51
221_A	228_A	0.511	0.51
197_E	207_F	0.509	0.51
124_L	153_I	0.508	0.50
114_L	120_R	0.507	0.50
17_R	37_L	0.507	0.50
76_V	240_K	0.506	0.50
20_H	26_P	0.505	0.50
102_L	215_S	0.505	0.50
177_G	209_H	0.505	0.50
273_L	280_D	0.505	0.50
127_S	201_S	0.503	0.50
16_A	23_Y	0.502	0.50
210_V	267_L	0.502	0.50
242_A	247_E	0.500	0.49

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
3ieiA	2	0.8487	100	0.374	Contact Map
1rjdA	1	0.9243	100	0.384	Contact Map
2uyoA	1	0.8586	100	0.385	Contact Map
2zwaA	1	0.9178	100	0.396	Contact Map
3giwA	1	0.8224	99	0.834	Contact Map
2qe6A	2	0.8322	98.8	0.848	Contact Map
2r3sA	4	0.8783	98.1	0.878	Contact Map
3dp7A	2	0.898	98	0.882	Contact Map
2ip2A	2	0.8355	98	0.882	Contact Map
3g2mA	2	0.7039	97.9	0.883	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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