YAFP - ECOLI - GREMLIN Contacts

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YAFP - Uncharacterized N-acetyltransferase YafP

UniProt:	Q47158	Sequences: MNNIQIRNYQPGDFQQLCAIFIRAVTMTASQHYSPQQISAWAQIDESRWKEKLAKSQVWVAIINAQPVGFISRIEHYIDMLFVDPEYTRRGVASALLKPLIKSESELTVDASITAKPFFERYGFQTVKQQRVECRGAWFTNFYMRYKPQH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13153
Length:	150 (142)
Sequences:	3850 (3109)
Seq/√Len:	260.9

ECOLI - YAFP YIAC YJAB YJGM RIMI PHNO MNAT YEDL YPEA
BACSU - YTMI PAIA YUAI YWNH YESJ RIMI YHFO YSNE YQJY YBFA YYAR YHDJ YRKN
HALSA - Q9HRK6 Q9HSL3 Q9HMF0 Q9HMI8
SULSO - Y209 Q7LXZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_S	122_Y	3.422	1.00
7_R	62_I	3.010	1.00
23_R	84_D	2.976	1.00
101_I	124_F	2.770	1.00
7_R	13_D	2.750	1.00
116_K	120_E	2.701	1.00
71_I	100_L	2.598	1.00
106_E	145_R	2.534	1.00
97_L	122_Y	2.497	1.00
61_A	92_V	2.414	1.00
59_W	99_P	2.380	1.00
71_I	78_I	2.235	1.00
68_V	87_Y	2.211	1.00
35_P	39_S	2.205	1.00
19_A	23_R	2.091	1.00
99_P	102_K	1.909	1.00
22_I	26_T	1.880	1.00
69_G	83_V	1.846	1.00
20_I	67_P	1.815	1.00
117_P	120_E	1.800	1.00
23_R	85_P	1.770	1.00
127_V	145_R	1.755	1.00
34_S	37_Q	1.745	1.00
9_Y	17_L	1.649	1.00
60_V	67_P	1.638	1.00
120_E	126_T	1.632	1.00
99_P	103_S	1.614	1.00
71_I	96_L	1.598	1.00
78_I	97_L	1.588	1.00
87_Y	90_R	1.579	1.00
62_I	65_A	1.575	1.00
63_I	68_V	1.452	1.00
63_I	90_R	1.436	1.00
16_Q	20_I	1.404	1.00
28_T	88_T	1.391	1.00
22_I	42_A	1.389	1.00
32_H	114_T	1.384	1.00
68_V	92_V	1.363	1.00
20_I	24_A	1.362	1.00
62_I	67_P	1.338	1.00
98_K	122_Y	1.309	1.00
24_A	88_T	1.283	1.00
69_G	92_V	1.268	1.00
63_I	87_Y	1.267	1.00
23_R	86_E	1.251	1.00
15_Q	46_E	1.247	1.00
14_F	18_C	1.244	1.00
56_S	72_S	1.210	1.00
105_S	109_V	1.189	1.00
116_K	126_T	1.175	1.00
128_K	143_Y	1.175	1.00
57_Q	103_S	1.146	1.00
6_I	59_W	1.143	1.00
126_T	142_F	1.142	1.00
131_R	138_W	1.126	1.00
11_P	54_A	1.118	1.00
94_S	98_K	1.113	1.00
30_S	38_I	1.106	1.00
7_R	60_V	1.096	1.00
16_Q	19_A	1.094	1.00
72_S	80_M	1.086	1.00
88_T	114_T	1.083	1.00
83_V	92_V	1.069	1.00
6_I	99_P	1.064	1.00
9_Y	60_V	1.050	1.00
130_Q	143_Y	1.048	1.00
129_Q	140_T	1.044	1.00
66_Q	87_Y	1.034	1.00
130_Q	141_N	1.032	1.00
126_T	129_Q	1.030	1.00
131_R	140_T	1.013	1.00
133_E	136_G	1.012	1.00
125_Q	145_R	0.993	1.00
26_T	38_I	0.989	1.00
120_E	144_M	0.987	1.00
9_Y	13_D	0.975	1.00
116_K	144_M	0.963	1.00
63_I	66_Q	0.963	1.00
52_K	80_M	0.961	1.00
96_L	100_L	0.927	1.00
9_Y	14_F	0.919	1.00
133_E	138_W	0.919	1.00
98_K	102_K	0.919	1.00
21_F	49_W	0.908	1.00
21_F	70_F	0.906	1.00
51_E	55_K	0.903	1.00
29_A	32_H	0.896	1.00
66_Q	86_E	0.885	1.00
24_A	83_V	0.874	1.00
21_F	80_M	0.869	1.00
8_N	103_S	0.854	1.00
98_K	101_I	0.854	1.00
16_Q	67_P	0.854	1.00
20_I	84_D	0.849	0.99
94_S	121_R	0.843	0.99
17_L	70_F	0.830	0.99
66_Q	84_D	0.822	0.99
25_V	82_F	0.819	0.99
77_Y	106_E	0.817	0.99
19_A	84_D	0.810	0.99
84_D	87_Y	0.807	0.99
15_Q	19_A	0.807	0.99
24_A	29_A	0.804	0.99
115_A	118_F	0.794	0.99
73_R	79_D	0.791	0.99
76_H	104_E	0.787	0.99
27_M	85_P	0.774	0.99
5_Q	8_N	0.768	0.99
44_I	49_W	0.767	0.99
23_R	27_M	0.764	0.99
25_V	32_H	0.763	0.99
77_Y	108_T	0.762	0.99
45_D	49_W	0.762	0.99
26_T	43_Q	0.760	0.99
73_R	104_E	0.757	0.99
107_L	124_F	0.754	0.99
40_A	137_A	0.753	0.99
21_F	25_V	0.753	0.99
78_I	81_L	0.752	0.99
37_Q	41_W	0.752	0.99
132_V	139_F	0.741	0.99
127_V	143_Y	0.739	0.99
29_A	38_I	0.739	0.99
101_I	122_Y	0.736	0.99
25_V	41_W	0.735	0.99
24_A	28_T	0.732	0.98
24_A	85_P	0.730	0.98
21_F	82_F	0.727	0.98
50_K	54_A	0.727	0.98
108_T	143_Y	0.723	0.98
9_Y	58_V	0.716	0.98
109_V	119_F	0.711	0.98
5_Q	62_I	0.710	0.98
26_T	35_P	0.707	0.98
17_L	67_P	0.706	0.98
126_T	144_M	0.704	0.98
116_K	142_F	0.703	0.98
97_L	124_F	0.703	0.98
16_Q	66_Q	0.697	0.98
113_I	142_F	0.696	0.98
61_A	68_V	0.696	0.98
104_E	107_L	0.695	0.98
49_W	53_L	0.688	0.98
89_R	121_R	0.686	0.98
13_D	60_V	0.681	0.98
37_Q	139_F	0.681	0.98
15_Q	50_K	0.680	0.98
77_Y	110_D	0.671	0.97
111_A	129_Q	0.670	0.97
52_K	79_D	0.669	0.97
25_V	29_A	0.667	0.97
61_A	69_G	0.665	0.97
8_N	57_Q	0.656	0.97
52_K	56_S	0.651	0.97
17_L	53_L	0.649	0.97
61_A	96_L	0.647	0.97
85_P	88_T	0.641	0.97
61_A	95_A	0.640	0.96
70_F	80_M	0.636	0.96
11_P	50_K	0.636	0.96
32_H	82_F	0.629	0.96
29_A	88_T	0.624	0.96
53_L	56_S	0.623	0.96
18_C	43_Q	0.621	0.96
31_Q	35_P	0.618	0.96
29_A	93_A	0.617	0.96
9_Y	53_L	0.617	0.96
4_I	63_I	0.611	0.95
58_V	72_S	0.610	0.95
83_V	96_L	0.608	0.95
59_W	103_S	0.606	0.95
14_F	49_W	0.600	0.95
118_F	122_Y	0.596	0.95
95_A	98_K	0.596	0.95
40_A	135_R	0.593	0.95
129_Q	142_F	0.590	0.95
82_F	118_F	0.590	0.95
26_T	39_S	0.588	0.94
87_Y	92_V	0.585	0.94
18_C	46_E	0.584	0.94
26_T	42_A	0.580	0.94
46_E	50_K	0.575	0.94
17_L	49_W	0.563	0.93
89_R	117_P	0.562	0.93
28_T	38_I	0.555	0.93
8_N	59_W	0.551	0.92
92_V	95_A	0.551	0.92
80_M	119_F	0.550	0.92
71_I	81_L	0.550	0.92
48_R	52_K	0.549	0.92
37_Q	137_A	0.549	0.92
49_W	52_K	0.549	0.92
132_V	137_A	0.548	0.92
113_I	117_P	0.546	0.92
52_K	72_S	0.539	0.91
78_I	104_E	0.535	0.91
39_S	43_Q	0.534	0.91
7_R	10_Q	0.533	0.91
97_L	101_I	0.533	0.91
36_Q	137_A	0.532	0.91
112_S	117_P	0.532	0.91
27_M	86_E	0.531	0.91
4_I	61_A	0.529	0.91
76_H	106_E	0.528	0.91
83_V	93_A	0.519	0.90
18_C	21_F	0.518	0.90
62_I	68_V	0.518	0.90
18_C	45_D	0.515	0.90
134_C	139_F	0.508	0.89
19_A	66_Q	0.507	0.89
38_I	42_A	0.506	0.89
93_A	114_T	0.501	0.88
97_L	100_L	0.500	0.88

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
2fiwA	2	0.9867	99.9	0.344	Contact Map
3fncA	2	0.9867	99.9	0.406	Contact Map
1tiqA	1	0.9867	99.9	0.406	Contact Map
3fixA	2	0.9333	99.9	0.413	Contact Map
4e2aA	2	0.98	99.9	0.413	Contact Map
1gheA	1	0.96	99.8	0.416	Contact Map
2oh1A	1	0.9067	99.8	0.42	Contact Map
3dr6A	2	0.9467	99.8	0.423	Contact Map
2j8mA	2	0.9467	99.8	0.426	Contact Map
2kcwA	1	0.9533	99.8	0.427	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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