YDAF - BACSU - GREMLIN Contacts

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YDAF - Putative ribosomal N-acetyltransferase YdaF

UniProt:	P96579	Sequences: MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREWEGEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	183 (167)
Sequences:	19949 (15263)
Seq/√Len:	1181.1

ECOLI - RIMJ ATDA RIML YHHY MNAT
BACSU - YDAF YJCK YOAA YOKL YNAD YKKB YJDG YWNH
HALSA - Q9HNJ3 Q9HMZ2 Q9HRY5 Q9HRY6 Q9HSL3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
111_T	147_R	2.901	1.00
132_I	145_P	2.892	1.00
13_R	73_L	2.683	1.00
13_R	19_D	2.605	1.00
33_R	102_K	2.513	1.00
153_E	173_S	2.425	1.00
9_H	112_A	2.368	1.00
94_A	127_L	2.366	1.00
134_A	142_R	2.288	1.00
84_L	121_A	2.264	1.00
152_E	155_K	2.260	1.00
134_A	145_P	2.131	1.00
143_A	146_E	2.124	1.00
7_N	116_K	2.113	1.00
152_E	170_V	2.088	1.00
7_N	112_A	2.062	1.00
142_R	146_E	2.014	1.00
119_T	123_E	1.996	1.00
71_G	78_L	1.866	1.00
96_I	114_C	1.855	1.00
31_Q	102_K	1.851	1.00
118_I	130_V	1.792	1.00
128_N	158_D	1.761	1.00
118_I	150_F	1.746	1.00
155_K	170_V	1.741	1.00
15_L	71_G	1.736	1.00
22_R	78_L	1.702	1.00
82_I	113_A	1.688	1.00
114_C	148_I	1.669	1.00
142_R	152_E	1.650	1.00
54_I	58_W	1.620	1.00
116_K	119_T	1.589	1.00
136_V	168_D	1.584	1.00
142_R	170_V	1.552	1.00
146_E	152_E	1.515	1.00
73_L	76_G	1.508	1.00
101_A	104_F	1.490	1.00
98_Y	145_P	1.480	1.00
100_I	110_I	1.472	1.00
5_K	116_K	1.441	1.00
139_E	142_R	1.438	1.00
17_P	56_P	1.415	1.00
128_N	166_H	1.394	1.00
111_T	144_V	1.372	1.00
20_A	52_E	1.368	1.00
79_C	104_F	1.345	1.00
6_V	11_T	1.332	1.00
121_A	130_V	1.320	1.00
22_R	77_S	1.301	1.00
11_T	73_L	1.300	1.00
120_Y	124_E	1.299	1.00
129_R	173_S	1.294	1.00
136_V	155_K	1.294	1.00
142_R	172_Y	1.289	1.00
82_I	117_L	1.286	1.00
161_Y	166_H	1.284	1.00
72_L	100_I	1.275	1.00
159_G	169_L	1.252	1.00
72_L	113_A	1.249	1.00
98_Y	141_S	1.207	1.00
26_L	101_A	1.200	1.00
156_A	171_Y	1.193	1.00
110_I	144_V	1.173	1.00
137_G	167_H	1.169	1.00
77_S	103_E	1.160	1.00
121_A	125_L	1.159	1.00
7_N	10_I	1.154	1.00
95_E	133_C	1.151	1.00
33_R	105_E	1.130	1.00
88_D	91_N	1.128	1.00
33_R	36_K	1.114	1.00
105_E	140_K	1.114	1.00
20_A	55_I	1.113	1.00
77_S	104_F	1.112	1.00
81_M	99_W	1.099	1.00
120_Y	125_L	1.094	1.00
52_E	56_P	1.076	1.00
5_K	12_I	1.071	1.00
134_A	172_Y	1.067	1.00
70_A	117_L	1.059	1.00
26_L	99_W	1.044	1.00
129_R	153_E	1.043	1.00
93_K	131_A	1.029	1.00
152_E	172_Y	1.029	1.00
5_K	120_Y	1.029	1.00
102_K	105_E	1.028	1.00
132_I	150_F	1.026	1.00
22_R	25_E	1.019	1.00
21_E	46_S	1.013	1.00
158_D	168_D	1.012	1.00
118_I	174_L	1.011	1.00
155_K	168_D	1.009	1.00
141_S	145_P	1.009	1.00
111_T	115_R	0.985	1.00
145_P	150_F	0.977	1.00
135_A	167_H	0.975	1.00
53_T	57_D	0.966	1.00
118_I	148_I	0.966	1.00
144_V	148_I	0.964	1.00
157_R	168_D	0.963	1.00
70_A	120_Y	0.953	1.00
11_T	76_G	0.953	1.00
157_R	173_S	0.951	1.00
73_L	78_L	0.942	1.00
150_F	174_L	0.931	1.00
17_P	52_E	0.919	1.00
139_E	143_A	0.909	1.00
106_G	140_K	0.907	1.00
121_A	127_L	0.905	1.00
19_D	73_L	0.903	1.00
136_V	170_V	0.902	1.00
34_L	105_E	0.895	1.00
111_T	148_I	0.895	1.00
115_R	119_T	0.894	1.00
84_L	117_L	0.891	1.00
10_I	113_A	0.882	1.00
112_A	116_K	0.875	1.00
17_P	20_A	0.867	1.00
37_W	135_A	0.866	1.00
92_R	166_H	0.865	1.00
98_Y	110_I	0.865	1.00
15_L	81_M	0.863	1.00
10_I	109_I	0.858	1.00
27_I	99_W	0.850	1.00
115_R	148_I	0.847	1.00
93_K	129_R	0.847	1.00
129_R	175_L	0.834	1.00
157_R	175_L	0.834	1.00
20_A	24_A	0.831	1.00
100_I	109_I	0.827	1.00
156_A	159_G	0.826	1.00
61_Q	66_N	0.823	1.00
17_P	59_R	0.820	1.00
21_E	25_E	0.809	1.00
25_E	77_S	0.796	1.00
93_K	159_G	0.794	1.00
146_E	172_Y	0.787	1.00
139_E	146_E	0.786	1.00
25_E	101_A	0.778	1.00
134_A	141_S	0.777	1.00
104_F	107_K	0.772	1.00
161_Y	165_M	0.770	1.00
95_E	131_A	0.770	1.00
161_Y	164_G	0.769	1.00
53_T	56_P	0.766	1.00
7_N	12_I	0.764	1.00
8_E	112_A	0.761	1.00
133_C	156_A	0.761	1.00
153_E	157_R	0.754	1.00
98_Y	114_C	0.742	1.00
158_D	166_H	0.741	1.00
106_G	111_T	0.736	1.00
132_I	141_S	0.736	1.00
47_A	52_E	0.729	1.00
61_Q	67_G	0.717	1.00
77_S	101_A	0.717	1.00
114_C	144_V	0.714	1.00
22_R	101_A	0.708	1.00
45_S	49_T	0.705	1.00
111_T	140_K	0.704	1.00
24_A	30_N	0.701	1.00
25_E	103_E	0.698	1.00
143_A	147_R	0.698	1.00
37_W	137_G	0.695	1.00
13_R	71_G	0.692	1.00
106_G	143_A	0.692	1.00
9_H	108_G	0.688	1.00
31_Q	105_E	0.683	1.00
21_E	47_A	0.682	1.00
26_L	78_L	0.682	1.00
134_A	170_V	0.682	1.00
110_I	114_C	0.680	1.00
79_C	109_I	0.679	1.00
14_L	62_Y	0.675	1.00
55_I	58_W	0.671	1.00
46_S	49_T	0.669	1.00
109_I	112_A	0.668	1.00
133_C	169_L	0.666	1.00
137_G	165_M	0.660	1.00
158_D	175_L	0.656	1.00
72_L	109_I	0.653	1.00
69_E	83_S	0.651	1.00
74_Y	109_I	0.648	1.00
98_Y	144_V	0.648	1.00
94_A	121_A	0.644	1.00
74_Y	79_C	0.644	1.00
140_K	143_A	0.637	1.00
41_A	44_P	0.636	1.00
10_I	112_A	0.634	1.00
145_P	172_Y	0.611	1.00
82_I	114_C	0.608	1.00
46_S	52_E	0.606	1.00
47_A	50_Y	0.606	1.00
35_G	38_L	0.606	1.00
136_V	142_R	0.603	1.00
72_L	82_I	0.602	1.00
84_L	94_A	0.602	1.00
162_V	165_M	0.599	1.00
72_L	80_G	0.596	1.00
34_L	99_W	0.596	1.00
151_L	157_R	0.593	1.00
58_W	69_E	0.592	1.00
100_I	105_E	0.590	1.00
40_F	43_N	0.587	1.00
106_G	144_V	0.584	1.00
129_R	159_G	0.584	1.00
38_L	99_W	0.579	1.00
21_E	24_A	0.575	1.00
92_R	128_N	0.575	1.00
13_R	16_E	0.572	1.00
85_H	95_E	0.571	1.00
78_L	81_M	0.571	1.00
16_E	19_D	0.571	1.00
43_N	49_T	0.568	1.00
100_I	104_F	0.568	1.00
162_V	167_H	0.566	1.00
98_Y	132_I	0.566	1.00
92_R	161_Y	0.565	1.00
131_A	156_A	0.562	1.00
148_I	174_L	0.559	1.00
35_G	42_E	0.551	1.00
114_C	150_F	0.550	1.00
94_A	130_V	0.550	1.00
31_Q	101_A	0.546	1.00
45_S	48_D	0.545	1.00
119_T	124_E	0.543	1.00
133_C	171_Y	0.541	1.00
22_R	26_L	0.540	1.00
131_A	159_G	0.538	1.00
132_I	172_Y	0.534	1.00
15_L	23_L	0.533	1.00
48_D	52_E	0.531	1.00
57_D	61_Q	0.525	1.00
23_L	81_M	0.523	1.00
83_S	97_G	0.523	1.00
32_Q	36_K	0.522	1.00
8_E	11_T	0.520	1.00
106_G	147_R	0.515	1.00
24_A	50_Y	0.513	1.00
100_I	113_A	0.512	1.00
92_R	126_E	0.512	1.00
55_I	59_R	0.512	1.00
38_L	41_A	0.511	1.00
31_Q	35_G	0.508	1.00
62_Y	68_I	0.507	1.00
118_I	122_F	0.506	1.00
22_R	73_L	0.504	1.00
96_I	130_V	0.503	1.00
65_L	68_I	0.501	1.00
160_L	169_L	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
1nslA	3	0.9727	100	0.278	Contact Map
2vzyA	3	0.8852	100	0.296	Contact Map
3pzjA	2	0.9508	100	0.303	Contact Map
3r9fA	1	0.9563	100	0.304	Contact Map
1yreA	2	0.9344	100	0.308	Contact Map
2z10A	2	0.9617	100	0.321	Contact Map
2fckA	2	0.9235	100	0.322	Contact Map
3igrA	2	0.9672	100	0.339	Contact Map
1s7kA	2	0.8579	100	0.343	Contact Map
4r9mA	5	0.918	100	0.348	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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