YODH - BACSU - GREMLIN Contacts

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YODH - Uncharacterized methyltransferase YodH

UniProt:	O34954	Sequences: MSRYLEMLSLFGVAGAHPGGLAFSKAVLQKAAPSPDQPILDAGCGTGQTAAYLGHLLYPVTVVDKDPIMLEKAKKRFANEGLAIPAYQAELEHLPFSSESFSCVLSESVLSFSRLTSSLQEISRVLKPSGMLIGIEAALKKPMPPAEKKQMMDFYGFTCLHEESEWHKLLRSYGFQKTEAMSLLPEDMEFEPTTEMDLSQTIDPIYYDTLQTHYQLMQLYSEYMGHCIFIAYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	233 (188)
Sequences:	18009 (13196)
Seq/√Len:	962.4

ECOLI - BIOC SMTA TAM UBIG YJHP UBIE CMOA YAFE TEHB CMOB RLMA CFA
BACSU - YODH YCGJ YXBB YBAJ MENG YRRT YRHH YQEM YDAC YXJB
HALSA - Q9HND6 Q9HRX3 Q9HMT2 Q9HR81 Q9HR63 ARSM Q9HSK6 Q9HQ85
SULSO - Q7LXN7 Q97WT7 Q97X57 Q97ZU8 Q97WH3 Q97WN4 Q97YX4 Q97XD7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_P	59_P	3.136	1.00
67_P	88_Q	2.707	1.00
123_S	175_F	2.532	1.00
44_C	62_V	2.504	1.00
121_E	124_R	2.367	1.00
50_A	60_V	2.311	1.00
61_T	101_F	2.311	1.00
70_L	86_A	2.255	1.00
116_T	172_S	2.253	1.00
122_I	132_L	2.233	1.00
63_V	89_A	2.232	1.00
73_A	86_A	2.142	1.00
37_Q	103_C	2.100	1.00
70_L	74_K	2.093	1.00
40_L	101_F	2.091	1.00
102_S	127_K	2.061	1.00
55_H	80_E	2.047	1.00
61_T	87_Y	2.043	1.00
104_V	122_I	2.017	1.00
96_F	101_F	2.015	1.00
59_P	85_P	1.992	1.00
70_L	88_Q	1.915	1.00
42_A	122_I	1.906	1.00
34_S	37_Q	1.844	1.00
104_V	126_L	1.836	1.00
72_K	75_K	1.816	1.00
51_A	77_F	1.810	1.00
67_P	71_E	1.789	1.00
116_T	120_Q	1.727	1.00
39_I	53_L	1.696	1.00
108_S	112_F	1.693	1.00
126_L	130_G	1.679	1.00
51_A	76_R	1.667	1.00
121_E	125_V	1.654	1.00
77_F	86_A	1.635	1.00
8_L	11_F	1.617	1.00
116_T	169_L	1.605	1.00
38_P	61_T	1.567	1.00
162_E	165_E	1.540	1.00
44_C	50_A	1.534	1.00
126_L	132_L	1.516	1.00
64_D	70_L	1.508	1.00
42_A	91_L	1.498	1.00
38_P	127_K	1.491	1.00
61_T	85_P	1.481	1.00
109_V	113_S	1.472	1.00
115_L	169_L	1.456	1.00
25_K	52_Y	1.436	1.00
50_A	62_V	1.424	1.00
68_I	71_E	1.408	1.00
114_R	117_S	1.397	1.00
89_A	95_P	1.391	1.00
167_H	171_R	1.368	1.00
126_L	175_F	1.353	1.00
110_L	113_S	1.336	1.00
152_M	156_G	1.317	1.00
109_V	112_F	1.289	1.00
75_K	79_N	1.287	1.00
77_F	82_L	1.278	1.00
90_E	93_H	1.277	1.00
5_L	68_I	1.265	1.00
52_Y	55_H	1.264	1.00
5_L	66_D	1.252	1.00
62_V	86_A	1.248	1.00
52_Y	56_L	1.223	1.00
97_S	100_S	1.211	1.00
117_S	120_Q	1.193	1.00
25_K	29_Q	1.189	1.00
38_P	101_F	1.178	1.00
39_I	103_C	1.177	1.00
33_P	37_Q	1.175	1.00
119_L	170_L	1.171	1.00
98_S	124_R	1.167	1.00
167_H	180_A	1.166	1.00
77_F	84_I	1.161	1.00
65_K	90_E	1.161	1.00
38_P	102_S	1.158	1.00
71_E	74_K	1.147	1.00
63_V	94_L	1.136	1.00
51_A	80_E	1.133	1.00
87_Y	96_F	1.126	1.00
43_G	106_S	1.126	1.00
40_L	104_V	1.126	1.00
108_S	111_S	1.124	1.00
25_K	56_L	1.118	1.00
168_K	172_S	1.113	1.00
152_M	155_Y	1.106	1.00
76_R	79_N	1.103	1.00
168_K	171_R	1.092	1.00
94_L	121_E	1.090	1.00
95_P	121_E	1.084	1.00
118_S	122_I	1.083	1.00
78_A	83_A	1.070	1.00
154_F	157_F	1.062	1.00
116_T	173_Y	1.049	1.00
26_A	29_Q	1.041	1.00
123_S	173_Y	1.039	1.00
75_K	78_A	1.037	1.00
46_T	69_M	1.029	1.00
62_V	73_A	1.027	1.00
43_G	108_S	1.022	1.00
26_A	181_M	1.020	1.00
44_C	73_A	1.012	1.00
104_V	125_V	1.008	1.00
112_F	118_S	1.007	1.00
51_A	55_H	1.004	1.00
15_G	18_P	1.001	1.00
27_V	133_I	0.983	1.00
30_K	179_E	0.981	1.00
47_G	73_A	0.978	1.00
153_D	157_F	0.974	1.00
37_Q	58_Y	0.970	1.00
94_L	125_V	0.967	1.00
38_P	100_S	0.959	1.00
74_K	78_A	0.946	1.00
39_I	105_L	0.943	1.00
122_I	126_L	0.941	1.00
43_G	109_V	0.936	1.00
30_K	181_M	0.936	1.00
153_D	156_G	0.930	1.00
64_D	69_M	0.923	1.00
53_L	105_L	0.918	1.00
107_E	110_L	0.916	1.00
26_A	30_K	0.903	1.00
36_D	58_Y	0.900	1.00
117_S	121_E	0.898	1.00
163_E	182_S	0.887	1.00
20_G	23_F	0.886	1.00
106_S	109_V	0.882	1.00
49_T	105_L	0.881	1.00
50_A	86_A	0.881	1.00
151_M	154_F	0.880	1.00
72_K	76_R	0.870	1.00
61_T	96_F	0.869	1.00
107_E	112_F	0.866	1.00
50_A	84_I	0.865	1.00
66_D	69_M	0.861	1.00
76_R	80_E	0.854	1.00
29_Q	56_L	0.852	1.00
16_A	20_G	0.834	1.00
120_Q	173_Y	0.823	1.00
143_M	148_K	0.820	1.00
63_V	87_Y	0.819	1.00
107_E	111_S	0.815	1.00
71_E	75_K	0.815	1.00
5_L	8_L	0.813	1.00
44_C	64_D	0.810	1.00
37_Q	102_S	0.805	1.00
41_D	62_V	0.803	1.00
100_S	127_K	0.799	1.00
48_Q	52_Y	0.792	1.00
54_G	84_I	0.791	1.00
107_E	135_I	0.790	1.00
151_M	156_G	0.789	1.00
41_D	60_V	0.785	1.00
89_A	94_L	0.775	1.00
146_A	149_K	0.771	1.00
148_K	151_M	0.766	1.00
19_G	23_F	0.757	1.00
147_E	150_Q	0.755	1.00
8_L	12_G	0.753	1.00
108_S	113_S	0.747	1.00
47_G	86_A	0.747	1.00
177_K	180_A	0.746	1.00
165_E	168_K	0.740	1.00
28_L	53_L	0.735	1.00
40_L	125_V	0.734	1.00
110_L	136_E	0.732	1.00
163_E	180_A	0.729	1.00
146_A	150_Q	0.723	1.00
39_I	60_V	0.722	1.00
33_P	36_D	0.720	1.00
144_P	150_Q	0.716	1.00
144_P	147_E	0.714	1.00
42_A	104_V	0.708	1.00
28_L	56_L	0.707	1.00
55_H	82_L	0.704	1.00
92_E	114_R	0.702	1.00
4_Y	7_M	0.700	1.00
17_H	20_G	0.699	1.00
103_C	131_M	0.699	1.00
51_A	54_G	0.695	1.00
136_E	166_W	0.692	1.00
16_A	19_G	0.691	1.00
96_F	125_V	0.689	1.00
98_S	125_V	0.688	1.00
17_H	21_L	0.688	1.00
152_M	157_F	0.687	1.00
119_L	173_Y	0.685	1.00
74_K	85_P	0.685	1.00
21_L	25_K	0.682	1.00
109_V	136_E	0.682	1.00
148_K	153_D	0.682	1.00
21_L	24_S	0.677	1.00
14_A	22_A	0.676	1.00
68_I	72_K	0.669	1.00
151_M	155_Y	0.664	1.00
123_S	174_G	0.662	1.00
22_A	25_K	0.661	1.00
147_E	151_M	0.660	1.00
119_L	169_L	0.660	1.00
74_K	86_A	0.660	1.00
103_C	130_G	0.659	1.00
46_T	76_R	0.659	1.00
62_V	84_I	0.655	1.00
120_Q	124_R	0.655	1.00
49_T	53_L	0.651	1.00
92_E	113_S	0.649	1.00
39_I	58_Y	0.647	1.00
150_Q	153_D	0.646	1.00
12_G	16_A	0.644	1.00
148_K	152_M	0.641	1.00
67_P	74_K	0.639	1.00
41_D	44_C	0.639	1.00
100_S	125_V	0.635	1.00
32_A	131_M	0.635	1.00
18_P	21_L	0.632	1.00
164_S	168_K	0.630	1.00
54_G	82_L	0.626	1.00
163_E	167_H	0.625	1.00
169_L	173_Y	0.616	1.00
4_Y	8_L	0.614	1.00
51_A	82_L	0.608	1.00
165_E	169_L	0.607	1.00
150_Q	155_Y	0.606	1.00
11_F	14_A	0.605	1.00
33_P	58_Y	0.604	1.00
98_S	121_E	0.603	1.00
143_M	147_E	0.602	1.00
108_S	135_I	0.601	1.00
65_K	88_Q	0.601	1.00
132_L	175_F	0.600	1.00
24_S	49_T	0.599	1.00
94_L	101_F	0.598	1.00
101_F	125_V	0.597	1.00
42_A	63_V	0.596	1.00
145_P	149_K	0.593	1.00
145_P	148_K	0.590	1.00
77_F	81_G	0.589	1.00
132_L	170_L	0.589	1.00
119_L	166_W	0.587	1.00
131_M	134_G	0.585	1.00
18_P	22_A	0.582	1.00
107_E	113_S	0.581	1.00
96_F	100_S	0.579	1.00
149_K	153_D	0.576	1.00
9_S	72_K	0.570	1.00
14_A	20_G	0.562	1.00
41_D	105_L	0.557	1.00
38_P	99_E	0.552	1.00
170_L	173_Y	0.551	1.00
20_G	24_S	0.550	1.00
51_A	86_A	0.548	1.00
93_H	117_S	0.546	1.00
31_A	133_I	0.545	1.00
138_A	141_K	0.544	1.00
42_A	118_S	0.543	1.00
16_A	24_S	0.541	1.00
48_Q	76_R	0.540	1.00
147_E	152_M	0.540	1.00
44_C	70_L	0.539	1.00
95_P	125_V	0.536	1.00
113_S	118_S	0.532	1.00
43_G	65_K	0.531	1.00
92_E	118_S	0.530	1.00
93_H	121_E	0.530	1.00
14_A	18_P	0.529	1.00
50_A	54_G	0.525	1.00
92_E	117_S	0.523	1.00
110_L	118_S	0.519	1.00
9_S	75_K	0.518	1.00
49_T	52_Y	0.516	1.00
37_Q	131_M	0.513	1.00
115_L	161_H	0.512	1.00
41_D	63_V	0.512	1.00
28_L	57_L	0.512	1.00
38_P	58_Y	0.512	1.00
171_R	177_K	0.507	1.00
145_P	151_M	0.506	1.00
91_L	118_S	0.504	1.00
36_D	102_S	0.503	1.00
169_L	172_S	0.500	1.00

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
4pneA	2	0.9914	100	0.381	Contact Map
3kkzA	2	0.9871	100	0.39	Contact Map
2o57A	2	1	100	0.393	Contact Map
3busA	1	0.9442	100	0.395	Contact Map
5bp7A	3	0.9914	100	0.401	Contact Map
2fk8A	1	0.9614	100	0.413	Contact Map
3f4kA	2	0.9871	100	0.414	Contact Map
3vc1A	5	0.9571	100	0.419	Contact Map
1vl5A	1	0.9142	100	0.419	Contact Map
2yqzA	1	0.9914	100	0.42	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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