YQEM - BACSU - GREMLIN Contacts

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YQEM - Putative methyltransferase YqeM

UniProt:	P54458	Sequences: MIYQGFASVYDELMSHAPYDQWTKWIEASLPEKGRILDLACGTGEISIRLAEKGFEVTGIDLSEEMLSFAQQKVSSSQPILFLQQDMREITGFDGQFDAVVICCDSLNYLKTKNDVIETFKSVFRVLKPEGILLFDVHSSFKIAEVFPDSTFADQDEDISYIWQSFAGSDELSVIHDMSFFVWNGEAYDRFDETHEQRTFPVEEYEEMLKNCGFQLHRVTADFTDTEPSAQSERLFFKAQKSKTIVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	247 (209)
Sequences:	7134 (5973)
Seq/√Len:	413.2

ECOLI - UBIE BIOC UBIG CMOA TAM SMTA YJHP TEHB RLMA YAFE
BACSU - YQEM YBAJ MENG YCGJ YXBB YODH YRRT YRHH YDAC YXJB
HALSA - Q9HR81 Q9HRX3 Q9HND6 Q9HMT2 Q9HR63 ARSM Q9HQ85
SULSO - Q97WN4 Q7LXN7 Q97ZU8 Q97WT7 Q97XD7 Q97X57 Q97YX4 Q97WH3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_L	84_Q	3.321	1.00
35_R	56_E	3.303	1.00
58_T	97_F	3.206	1.00
98_D	128_K	3.148	1.00
123_V	133_L	2.944	1.00
64_E	84_Q	2.899	1.00
37_L	97_F	2.888	1.00
47_S	57_V	2.829	1.00
122_S	125_R	2.721	1.00
70_A	82_F	2.689	1.00
40_A	106_S	2.590	1.00
67_L	82_F	2.431	1.00
39_L	123_V	2.418	1.00
41_C	59_G	2.277	1.00
64_E	68_S	2.221	1.00
88_R	115_D	2.181	1.00
61_D	67_L	2.086	1.00
56_E	81_L	2.078	1.00
91_T	122_S	2.057	1.00
58_T	83_L	2.051	1.00
74_V	82_F	1.997	1.00
36_I	50_L	1.983	1.00
117_I	211_N	1.973	1.00
60_I	85_Q	1.873	1.00
48_I	74_V	1.854	1.00
69_F	72_Q	1.834	1.00
100_V	127_L	1.781	1.00
48_I	73_K	1.761	1.00
35_R	128_K	1.721	1.00
100_V	123_V	1.719	1.00
122_S	126_V	1.710	1.00
119_T	123_V	1.688	1.00
40_A	102_I	1.673	1.00
90_I	122_S	1.649	1.00
35_R	95_G	1.642	1.00
47_S	59_G	1.630	1.00
74_V	78_Q	1.625	1.00
110_L	119_T	1.620	1.00
11_D	43_T	1.614	1.00
60_I	90_I	1.604	1.00
127_L	131_G	1.591	1.00
27_E	53_K	1.578	1.00
35_R	98_D	1.559	1.00
201_P	204_E	1.524	1.00
96_Q	128_K	1.517	1.00
19_Y	22_W	1.509	1.00
39_L	87_M	1.505	1.00
36_I	55_F	1.504	1.00
74_V	80_I	1.493	1.00
11_D	73_K	1.477	1.00
59_G	70_A	1.445	1.00
36_I	101_V	1.442	1.00
87_M	106_S	1.440	1.00
24_K	53_K	1.420	1.00
206_E	210_K	1.408	1.00
117_I	121_K	1.396	1.00
118_E	121_K	1.391	1.00
41_C	70_A	1.384	1.00
24_K	28_A	1.381	1.00
20_D	49_R	1.377	1.00
58_T	81_L	1.367	1.00
65_E	68_S	1.329	1.00
41_C	47_S	1.319	1.00
127_L	133_L	1.317	1.00
51_A	80_I	1.305	1.00
93_F	126_V	1.292	1.00
46_I	103_C	1.284	1.00
39_L	119_T	1.284	1.00
124_F	214_F	1.279	1.00
36_I	99_A	1.275	1.00
207_E	211_N	1.265	1.00
86_D	89_E	1.260	1.00
26_I	103_C	1.259	1.00
35_R	58_T	1.240	1.00
48_I	52_E	1.239	1.00
93_F	96_Q	1.238	1.00
67_L	71_Q	1.202	1.00
59_G	82_F	1.194	1.00
100_V	126_V	1.189	1.00
109_Y	195_H	1.173	1.00
62_L	86_D	1.171	1.00
47_S	82_F	1.170	1.00
41_C	61_D	1.168	1.00
49_R	52_E	1.166	1.00
111_K	115_D	1.163	1.00
37_L	100_V	1.156	1.00
202_V	206_E	1.150	1.00
30_L	99_A	1.121	1.00
118_E	122_S	1.105	1.00
74_V	77_S	1.099	1.00
38_D	101_V	1.082	1.00
204_E	207_E	1.069	1.00
52_E	78_Q	1.058	1.00
116_V	208_M	1.055	1.00
91_T	126_V	1.055	1.00
40_A	87_M	1.054	1.00
35_R	97_F	1.033	1.00
93_F	97_F	1.032	1.00
71_Q	75_S	1.027	1.00
34_G	55_F	1.026	1.00
34_G	99_A	1.025	1.00
91_T	125_R	1.022	1.00
121_K	125_R	1.020	1.00
146_V	150_S	1.018	1.00
123_V	127_L	1.018	1.00
115_D	118_E	1.008	1.00
22_W	26_I	1.001	1.00
117_I	208_M	1.001	1.00
63_S	66_M	1.001	1.00
137_V	205_Y	0.976	1.00
43_T	66_M	0.974	1.00
147_F	150_S	0.968	1.00
69_F	73_K	0.962	1.00
35_R	96_Q	0.960	1.00
13_L	16_H	0.957	1.00
38_D	59_G	0.954	1.00
39_L	60_I	0.953	1.00
75_S	78_Q	0.951	1.00
146_V	149_D	0.948	1.00
87_M	110_L	0.942	1.00
207_E	210_K	0.940	1.00
68_S	71_Q	0.939	1.00
18_P	22_W	0.935	1.00
171_E	175_I	0.926	1.00
20_D	24_K	0.926	1.00
94_D	126_V	0.921	1.00
23_T	27_E	0.916	1.00
107_L	120_F	0.916	1.00
25_W	28_A	0.916	1.00
49_R	53_K	0.908	1.00
51_A	78_Q	0.903	1.00
45_E	49_R	0.894	1.00
203_E	206_E	0.894	1.00
136_D	139_S	0.894	1.00
45_E	73_K	0.891	1.00
104_C	109_Y	0.884	1.00
68_S	72_Q	0.882	1.00
108_N	138_H	0.879	1.00
21_Q	24_K	0.874	1.00
168_G	171_E	0.873	1.00
138_H	141_F	0.869	1.00
206_E	219_V	0.866	1.00
90_I	126_V	0.866	1.00
96_Q	126_V	0.865	1.00
113_K	204_E	0.864	1.00
107_L	116_V	0.863	1.00
97_F	126_V	0.858	1.00
107_L	110_L	0.848	1.00
22_W	25_W	0.847	1.00
155_Q	159_I	0.845	1.00
146_V	151_T	0.836	1.00
51_A	79_P	0.835	1.00
18_P	21_Q	0.831	1.00
156_D	159_I	0.831	1.00
202_V	219_V	0.828	1.00
106_S	110_L	0.822	1.00
104_C	108_N	0.818	1.00
60_I	83_L	0.815	1.00
94_D	125_R	0.806	1.00
154_D	158_D	0.802	1.00
145_E	149_D	0.800	1.00
48_I	82_F	0.795	1.00
155_Q	160_S	0.790	1.00
176_H	180_F	0.786	1.00
163_W	166_F	0.785	1.00
34_G	98_D	0.779	1.00
10_Y	13_L	0.778	1.00
102_I	106_S	0.770	1.00
107_L	135_F	0.769	1.00
47_S	51_A	0.766	1.00
36_I	57_V	0.763	1.00
25_W	29_S	0.756	1.00
178_M	181_F	0.756	1.00
172_L	176_H	0.756	1.00
157_E	160_S	0.755	1.00
9_V	13_L	0.749	1.00
43_T	69_F	0.745	1.00
125_R	128_K	0.743	1.00
48_I	78_Q	0.742	1.00
113_K	117_I	0.739	1.00
47_S	80_I	0.733	1.00
26_I	134_L	0.724	1.00
19_Y	23_T	0.724	1.00
155_Q	158_D	0.720	1.00
61_D	82_F	0.720	1.00
117_I	212_C	0.714	1.00
177_D	181_F	0.707	1.00
175_I	178_M	0.706	1.00
173_S	176_H	0.705	1.00
153_A	157_E	0.699	1.00
85_Q	122_S	0.696	1.00
11_D	16_H	0.693	1.00
99_A	132_I	0.690	1.00
40_A	62_L	0.688	1.00
114_N	117_I	0.685	1.00
88_R	118_E	0.684	1.00
120_F	124_F	0.681	1.00
113_K	198_R	0.677	1.00
38_D	41_C	0.676	1.00
17_A	20_D	0.674	1.00
10_Y	14_M	0.672	0.99
173_S	177_D	0.669	0.99
75_S	79_P	0.668	0.99
174_V	178_M	0.668	0.99
46_I	101_V	0.665	0.99
95_G	126_V	0.662	0.99
71_Q	81_L	0.661	0.99
116_V	120_F	0.660	0.99
62_L	84_Q	0.659	0.99
159_I	162_I	0.658	0.99
61_D	66_M	0.657	0.99
120_F	133_L	0.656	0.99
38_D	104_C	0.654	0.99
203_E	207_E	0.652	0.99
47_S	50_L	0.651	0.99
85_Q	91_T	0.650	0.99
96_Q	125_R	0.649	0.99
144_A	147_F	0.647	0.99
71_Q	74_V	0.647	0.99
17_A	23_T	0.647	0.99
171_E	176_H	0.643	0.99
11_D	14_M	0.634	0.99
145_E	152_F	0.629	0.99
46_I	50_L	0.628	0.99
171_E	174_V	0.622	0.99
107_L	137_V	0.620	0.99
100_V	131_G	0.618	0.99
87_M	102_I	0.618	0.99
85_Q	90_I	0.611	0.99
43_T	73_K	0.611	0.99
62_L	87_M	0.609	0.99
104_C	138_H	0.608	0.99
23_T	26_I	0.607	0.99
210_K	216_L	0.606	0.99
113_K	208_M	0.605	0.99
113_K	207_E	0.603	0.99
26_I	30_L	0.600	0.99
195_H	199_T	0.599	0.99
64_E	71_Q	0.599	0.99
177_D	194_T	0.599	0.99
208_M	212_C	0.598	0.99
95_G	125_R	0.597	0.99
8_S	69_F	0.596	0.99
17_A	21_Q	0.594	0.99
174_V	177_D	0.594	0.99
187_A	191_F	0.593	0.99
157_E	163_W	0.593	0.99
56_E	95_G	0.592	0.99
148_P	151_T	0.591	0.99
39_L	100_V	0.591	0.99
107_L	119_T	0.589	0.99
38_D	57_V	0.588	0.99
108_N	137_V	0.587	0.99
37_L	126_V	0.583	0.99
109_Y	116_V	0.582	0.99
95_G	128_K	0.582	0.99
166_F	169_S	0.582	0.99
102_I	116_V	0.581	0.99
144_A	150_S	0.579	0.98
89_E	122_S	0.579	0.98
20_D	23_T	0.579	0.98
91_T	94_D	0.579	0.98
90_I	93_F	0.577	0.98
176_H	179_S	0.577	0.98
88_R	119_T	0.577	0.98
216_L	219_V	0.571	0.98
103_C	108_N	0.570	0.98
198_R	204_E	0.567	0.98
184_N	187_A	0.564	0.98
125_R	129_P	0.563	0.98
9_V	14_M	0.561	0.98
145_E	148_P	0.560	0.98
191_F	195_H	0.560	0.98
119_T	122_S	0.560	0.98
46_I	49_R	0.558	0.98
33_K	98_D	0.558	0.98
176_H	181_F	0.556	0.98
120_F	135_F	0.555	0.98
180_F	183_W	0.550	0.98
154_D	159_I	0.549	0.98
11_D	69_F	0.544	0.98
44_G	57_V	0.541	0.98
72_Q	75_S	0.540	0.98
132_I	217_H	0.540	0.98
71_Q	82_F	0.537	0.98
25_W	220_T	0.535	0.98
108_N	200_F	0.534	0.97
27_E	31_P	0.534	0.97
14_M	19_Y	0.534	0.97
102_I	135_F	0.533	0.97
38_D	102_I	0.531	0.97
188_Y	195_H	0.530	0.97
199_T	202_V	0.526	0.97
144_A	149_D	0.525	0.97
161_Y	165_S	0.524	0.97
186_E	189_D	0.524	0.97
22_W	103_C	0.524	0.97
179_S	183_W	0.522	0.97
147_F	151_T	0.521	0.97
87_M	119_T	0.518	0.97
172_L	175_I	0.517	0.97
85_Q	89_E	0.515	0.97
167_A	172_L	0.512	0.97
175_I	180_F	0.512	0.97
139_S	142_K	0.511	0.97
61_D	84_Q	0.508	0.97
136_D	140_S	0.507	0.97
36_I	54_G	0.506	0.97
22_W	29_S	0.506	0.97
141_F	145_E	0.503	0.96
106_S	109_Y	0.502	0.96
38_D	46_I	0.501	0.96
108_N	136_D	0.501	0.96
200_F	208_M	0.500	0.96

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
1y8cA	1	0.9717	100	0.333	Contact Map
3d2lA	1	0.9717	100	0.346	Contact Map
4hgzA	4	0.9271	100	0.384	Contact Map
3thrA	3	0.9798	100	0.407	Contact Map
1wznA	4	0.9312	100	0.41	Contact Map
3bxoA	2	0.915	100	0.42	Contact Map
5bszA	3	0.9312	100	0.427	Contact Map
3pfgA	2	0.9271	100	0.436	Contact Map
3g2mA	2	0.8785	100	0.44	Contact Map
1ri5A	1	0.8502	100	0.454	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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