YNAD - BACSU - GREMLIN Contacts

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YNAD - Uncharacterized N-acetyltransferase YnaD

UniProt:	P94482	Sequences: MHITTKRLLIREFEFKDWQAVYEYTSDSNVMKYIPEGVFTEEDAKAFVNKNKGDNAEKFPVILRDEDCLIGHIVFYKYFGEHTYEIGWVFNPNYQNKGYASEAAQAILEYGFKEMNLHRIIATCQPENIPSYRVMKKIGMRREGFFKKCIPKGNEWWDEYYYAILEEEWN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	170 (161)
Sequences:	19802 (15182)
Seq/√Len:	1196.5

ECOLI - RIMJ ATDA RIML YHHY MNAT
BACSU - YNAD YJCK YOKL YDAF YOAA YKKB YJDG YWNH
HALSA - Q9HMZ2 Q9HRY6 Q9HNJ3 Q9HRY5 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
122_A	135_M	2.747	1.00
101_S	137_K	2.708	1.00
11_R	62_I	2.708	1.00
63_L	66_E	2.437	1.00
11_R	17_D	2.384	1.00
143_E	163_A	2.266	1.00
84_Y	117_L	2.213	1.00
4_T	64_R	2.204	1.00
7_R	102_E	2.126	1.00
29_N	92_P	2.117	1.00
124_C	132_Y	2.096	1.00
75_F	111_G	2.093	1.00
142_R	145_F	2.075	1.00
142_R	160_Y	2.006	1.00
5_T	106_A	1.955	1.00
133_R	136_K	1.938	1.00
124_C	135_M	1.938	1.00
132_Y	136_K	1.890	1.00
109_E	113_K	1.843	1.00
5_T	102_E	1.802	1.00
60_P	69_L	1.748	1.00
27_D	92_P	1.743	1.00
118_H	148_K	1.740	1.00
86_I	104_A	1.721	1.00
108_L	140_M	1.686	1.00
13_F	60_P	1.677	1.00
108_L	120_I	1.667	1.00
19_Q	41_E	1.626	1.00
145_F	160_Y	1.601	1.00
20_A	69_L	1.589	1.00
91_N	94_Y	1.573	1.00
104_A	138_I	1.556	1.00
62_I	67_D	1.549	1.00
9_L	64_R	1.546	1.00
41_E	45_K	1.545	1.00
18_W	45_K	1.544	1.00
132_Y	142_R	1.537	1.00
73_I	103_A	1.520	1.00
106_A	109_E	1.496	1.00
126_P	158_D	1.485	1.00
132_Y	160_Y	1.445	1.00
151_P	156_W	1.442	1.00
90_F	100_A	1.420	1.00
136_K	142_R	1.409	1.00
15_F	49_N	1.372	1.00
118_H	156_W	1.357	1.00
47_F	51_N	1.352	1.00
129_I	132_Y	1.345	1.00
40_T	43_D	1.344	1.00
61_V	90_F	1.319	1.00
101_S	134_V	1.309	1.00
88_W	135_M	1.296	1.00
61_V	103_A	1.284	1.00
70_I	94_Y	1.236	1.00
111_G	120_I	1.230	1.00
132_Y	162_Y	1.229	1.00
126_P	145_F	1.226	1.00
20_A	68_C	1.218	1.00
9_L	62_I	1.201	1.00
149_C	159_E	1.192	1.00
73_I	107_I	1.190	1.00
63_L	70_I	1.185	1.00
119_R	163_A	1.182	1.00
110_Y	114_E	1.179	1.00
4_T	9_L	1.179	1.00
127_E	157_W	1.176	1.00
63_L	99_Y	1.166	1.00
68_C	93_N	1.137	1.00
146_F	161_Y	1.113	1.00
5_T	8_L	1.106	1.00
88_W	131_S	1.106	1.00
45_K	49_N	1.106	1.00
85_E	123_T	1.102	1.00
72_H	89_V	1.094	1.00
111_G	115_M	1.077	1.00
22_Y	41_E	1.059	1.00
100_A	134_V	1.054	1.00
68_C	94_Y	1.053	1.00
18_W	48_V	1.039	1.00
36_E	39_F	1.038	1.00
110_Y	115_M	1.036	1.00
147_K	163_A	1.030	1.00
131_S	135_M	1.028	1.00
92_P	95_Q	1.024	1.00
119_R	143_E	1.023	1.00
18_W	41_E	1.022	1.00
95_Q	130_P	1.016	1.00
24_Y	89_V	1.015	1.00
124_C	162_Y	1.010	1.00
148_K	158_D	1.010	1.00
20_A	23_E	0.995	1.00
145_F	158_D	0.989	1.00
147_K	158_D	0.989	1.00
15_F	45_K	0.978	1.00
24_Y	91_N	0.975	1.00
83_T	121_I	0.970	1.00
59_F	110_Y	0.964	1.00
142_R	162_Y	0.959	1.00
59_F	107_I	0.956	1.00
122_A	140_M	0.951	1.00
46_A	50_K	0.948	1.00
108_L	164_I	0.938	1.00
63_L	97_K	0.933	1.00
63_L	68_C	0.927	1.00
134_V	138_I	0.918	1.00
135_M	140_M	0.917	1.00
101_S	105_Q	0.906	1.00
125_Q	157_W	0.904	1.00
75_F	107_I	0.903	1.00
108_L	138_I	0.901	1.00
29_N	32_K	0.895	1.00
140_M	164_I	0.892	1.00
22_Y	26_S	0.890	1.00
129_I	133_R	0.879	1.00
39_F	44_A	0.872	1.00
111_G	117_L	0.870	1.00
105_Q	109_E	0.862	1.00
30_V	95_Q	0.852	1.00
90_F	99_Y	0.848	1.00
62_I	69_L	0.847	1.00
27_D	91_N	0.847	1.00
23_E	91_N	0.847	1.00
126_P	160_Y	0.842	1.00
101_S	138_I	0.842	1.00
82_H	156_W	0.838	1.00
13_F	72_H	0.837	1.00
8_L	103_A	0.832	1.00
96_N	130_P	0.826	1.00
9_L	67_D	0.825	1.00
83_T	119_R	0.825	1.00
8_L	99_Y	0.815	1.00
88_W	100_A	0.812	1.00
17_D	62_I	0.810	1.00
68_C	91_N	0.804	1.00
18_W	22_Y	0.804	1.00
102_E	106_A	0.804	1.00
143_E	147_K	0.797	1.00
27_D	93_N	0.796	1.00
105_Q	138_I	0.796	1.00
15_F	18_W	0.793	1.00
83_T	149_C	0.790	1.00
82_H	151_P	0.778	1.00
22_Y	44_A	0.777	1.00
19_Q	23_E	0.775	1.00
146_F	149_C	0.770	1.00
148_K	156_W	0.766	1.00
23_E	68_C	0.764	1.00
94_Y	97_K	0.763	1.00
29_N	95_Q	0.759	1.00
129_I	136_K	0.755	1.00
63_L	94_Y	0.754	1.00
136_K	162_Y	0.753	1.00
42_E	45_K	0.751	1.00
124_C	131_S	0.739	1.00
124_C	160_Y	0.723	1.00
104_A	134_V	0.720	1.00
123_T	146_F	0.713	1.00
23_E	93_N	0.711	1.00
41_E	44_A	0.709	1.00
96_N	101_S	0.708	1.00
85_E	121_I	0.706	1.00
5_T	10_I	0.705	1.00
20_A	91_N	0.702	1.00
151_P	155_E	0.698	1.00
25_T	89_V	0.688	1.00
42_E	46_A	0.684	1.00
46_A	49_N	0.678	1.00
33_Y	125_Q	0.677	1.00
43_D	46_A	0.676	1.00
31_M	34_I	0.670	1.00
122_A	131_S	0.668	1.00
11_R	60_P	0.667	1.00
88_W	104_A	0.665	1.00
70_I	99_Y	0.662	1.00
40_T	44_A	0.655	1.00
101_S	130_P	0.655	1.00
100_A	104_A	0.653	1.00
61_V	73_I	0.650	1.00
127_E	155_E	0.650	1.00
96_N	133_R	0.648	1.00
112_F	164_I	0.642	1.00
123_T	159_E	0.642	1.00
133_R	137_K	0.641	1.00
7_R	98_G	0.639	1.00
61_V	99_Y	0.636	1.00
24_Y	69_L	0.635	1.00
6_K	102_E	0.634	1.00
33_Y	127_E	0.628	1.00
84_Y	111_G	0.623	1.00
99_Y	102_E	0.622	1.00
23_E	27_D	0.620	1.00
58_K	74_V	0.617	1.00
27_D	95_Q	0.615	1.00
88_W	134_V	0.611	1.00
152_K	155_E	0.609	1.00
75_F	84_Y	0.605	1.00
34_I	89_V	0.592	1.00
82_H	118_H	0.591	1.00
130_P	133_R	0.590	1.00
135_M	162_Y	0.589	1.00
96_N	134_V	0.587	1.00
138_I	164_I	0.587	1.00
126_P	132_Y	0.586	1.00
61_V	71_G	0.585	1.00
11_R	14_E	0.578	1.00
90_F	95_Q	0.578	1.00
119_R	149_C	0.577	1.00
90_F	94_Y	0.576	1.00
8_L	102_E	0.570	1.00
151_P	154_N	0.569	1.00
73_I	104_A	0.568	1.00
14_E	17_D	0.565	1.00
150_I	159_E	0.562	1.00
44_A	47_F	0.559	1.00
13_F	21_V	0.557	1.00
141_R	147_K	0.552	1.00
108_L	112_F	0.549	1.00
104_A	140_M	0.548	1.00
123_T	161_Y	0.541	1.00
122_A	162_Y	0.539	1.00
121_I	149_C	0.538	1.00
21_V	72_H	0.538	1.00
30_V	89_V	0.534	1.00
69_L	72_H	0.530	1.00
152_K	157_W	0.529	1.00
144_G	163_A	0.524	1.00
144_G	147_K	0.522	1.00
8_L	106_A	0.519	1.00
121_I	146_F	0.517	1.00
19_Q	22_Y	0.516	1.00
76_Y	85_E	0.516	1.00
84_Y	120_I	0.516	1.00
25_T	72_H	0.513	1.00
70_I	91_N	0.506	1.00
25_T	39_F	0.506	1.00
20_A	62_I	0.506	1.00
51_N	58_K	0.506	1.00
18_W	44_A	0.505	1.00
109_E	114_E	0.505	1.00
86_I	120_I	0.502	1.00
120_I	140_M	0.501	1.00
44_A	48_V	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
3fbuA	2	0.9824	100	0.288	Contact Map
2vzyA	3	0.8941	100	0.294	Contact Map
3pzjA	2	0.9941	100	0.296	Contact Map
1yreA	2	0.9529	100	0.306	Contact Map
3r9fA	1	0.9647	100	0.318	Contact Map
2fckA	2	0.9647	100	0.321	Contact Map
2z10A	2	0.9824	100	0.324	Contact Map
3igrA	2	1	100	0.326	Contact Map
1nslA	3	0.9824	100	0.329	Contact Map
3tcvA	2	1	100	0.346	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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