YKUD - BACSU - GREMLIN Contacts

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YKUD - Putative L,D-transpeptidase YkuD

UniProt:	O34816	Sequences: MLTYQVKQGDTLNSIAADFRISTAALLQANPSLQAGLTAGQSIVIPGLPDPYTIPYHIAVSIGAKTLTLSLNNRVMKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSKQHYGIHGTNNPASIGKAVSKGCIRMHNKDVIELASIVPNGTRVTINR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	164 (149)
Sequences:	963 (619)
Seq/√Len:	50.7

ECOLI - YNHG YCFS YBIS ERFK
BACSU - YKUD YQJB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_Y	149_E	4.424	1.00
99_N	114_S	4.114	1.00
97_I	113_L	4.101	1.00
112_W	121_G	4.023	1.00
110_A	148_I	3.620	1.00
95_F	116_S	3.155	1.00
88_T	137_K	2.853	1.00
114_S	121_G	2.646	1.00
94_E	159_R	2.520	1.00
87_L	136_S	2.338	1.00
64_A	68_T	2.301	1.00
61_S	64_A	2.301	1.00
70_S	75_V	2.239	1.00
17_A	145_K	2.153	1.00
65_K	134_A	2.089	1.00
108_F	121_G	2.086	1.00
58_I	154_V	2.080	1.00
17_A	26_L	1.907	0.99
21_I	46_P	1.871	0.99
102_R	111_Y	1.823	0.99
111_Y	147_V	1.798	0.99
149_E	153_I	1.797	0.99
69_L	77_K	1.786	0.99
100_R	113_L	1.781	0.99
68_T	75_V	1.697	0.99
155_P	158_T	1.633	0.98
60_V	140_I	1.629	0.98
21_I	26_L	1.585	0.98
33_L	41_Q	1.534	0.97
82_A	136_S	1.533	0.97
66_T	78_T	1.425	0.96
95_F	117_K	1.416	0.95
142_M	147_V	1.412	0.95
104_P	107_P	1.412	0.95
85_K	88_T	1.369	0.94
112_W	147_V	1.364	0.94
61_S	68_T	1.318	0.93
57_H	70_S	1.301	0.93
77_K	149_E	1.286	0.92
130_S	135_V	1.281	0.92
82_A	87_L	1.261	0.92
67_L	122_I	1.250	0.91
16_A	26_L	1.241	0.91
66_T	131_I	1.231	0.91
126_N	131_I	1.215	0.90
69_L	150_L	1.210	0.90
66_T	83_V	1.204	0.90
59_A	70_S	1.186	0.89
45_I	72_N	1.183	0.89
67_L	81_I	1.177	0.89
69_L	153_I	1.173	0.88
111_Y	151_A	1.164	0.88
100_R	151_A	1.157	0.88
100_R	156_N	1.133	0.87
109_G	125_T	1.096	0.85
113_L	154_V	1.087	0.84
93_G	128_P	1.080	0.84
115_L	120_Y	1.079	0.84
103_N	110_A	1.075	0.84
154_V	158_T	1.073	0.83
111_Y	152_S	1.071	0.83
94_E	161_T	1.067	0.83
77_K	153_I	1.059	0.83
125_T	131_I	1.041	0.82
115_L	122_I	1.023	0.80
23_T	35_A	1.020	0.80
53_T	70_S	1.016	0.80
26_L	42_S	0.996	0.79
21_I	27_L	0.989	0.78
17_A	143_H	0.988	0.78
16_A	23_T	0.979	0.77
68_T	151_A	0.971	0.77
13_N	17_A	0.966	0.76
38_T	41_Q	0.954	0.76
104_P	125_T	0.949	0.75
110_A	144_N	0.948	0.75
31_P	34_Q	0.946	0.75
84_G	141_R	0.943	0.75
104_P	109_G	0.941	0.75
98_I	116_S	0.936	0.74
14_S	18_D	0.933	0.74
23_T	27_L	0.921	0.73
25_A	28_Q	0.909	0.72
65_K	136_S	0.907	0.72
56_Y	71_L	0.900	0.71
80_P	146_D	0.892	0.70
64_A	154_V	0.889	0.70
130_S	134_A	0.871	0.69
83_V	134_A	0.868	0.68
17_A	20_R	0.866	0.68
121_G	124_G	0.861	0.68
19_F	105_G	0.861	0.68
57_H	76_M	0.858	0.67
60_V	81_I	0.855	0.67
13_N	143_H	0.853	0.67
99_N	102_R	0.848	0.67
20_R	143_H	0.830	0.65
115_L	140_I	0.820	0.64
17_A	144_N	0.818	0.64
15_I	26_L	0.815	0.63
96_Y	157_G	0.815	0.63
122_I	128_P	0.808	0.63
13_N	19_F	0.806	0.63
49_P	78_T	0.805	0.62
18_D	27_L	0.799	0.62
80_P	107_P	0.790	0.61
113_L	155_P	0.787	0.61
72_N	94_E	0.781	0.60
22_S	130_S	0.766	0.59
44_V	152_S	0.765	0.59
74_R	94_E	0.763	0.58
67_L	115_L	0.761	0.58
88_T	106_G	0.760	0.58
62_I	83_V	0.760	0.58
72_N	155_P	0.758	0.58
68_T	132_G	0.745	0.57
24_A	32_S	0.743	0.56
85_K	143_H	0.743	0.56
40_G	96_Y	0.742	0.56
142_M	157_G	0.742	0.56
62_I	92_T	0.727	0.55
94_E	157_G	0.726	0.55
109_G	141_R	0.726	0.55
86_I	136_S	0.724	0.54
16_A	143_H	0.721	0.54
102_R	152_S	0.720	0.54
80_P	109_G	0.718	0.54
50_D	55_P	0.717	0.54
13_N	32_S	0.712	0.53
26_L	43_I	0.709	0.53
17_A	142_M	0.705	0.52
58_I	150_L	0.703	0.52
59_A	68_T	0.701	0.52
21_I	25_A	0.701	0.52
136_S	139_C	0.699	0.52
91_P	141_R	0.695	0.51
33_L	37_L	0.688	0.51
52_Y	152_S	0.687	0.51
96_Y	116_S	0.685	0.50
27_L	38_T	0.684	0.50
27_L	35_A	0.681	0.50
85_K	89_Q	0.679	0.50
87_L	137_K	0.679	0.50
87_L	90_T	0.679	0.50
96_Y	156_N	0.678	0.50
65_K	83_V	0.677	0.50
91_P	109_G	0.673	0.49
61_S	70_S	0.670	0.49
111_Y	148_I	0.667	0.49
43_I	98_I	0.656	0.47
61_S	148_I	0.654	0.47
106_G	131_I	0.652	0.47
68_T	78_T	0.652	0.47
14_S	22_S	0.651	0.47
15_I	153_I	0.647	0.46
58_I	132_G	0.645	0.46
104_P	108_F	0.645	0.46
45_I	154_V	0.645	0.46
131_I	141_R	0.641	0.46
133_K	143_H	0.634	0.45
116_S	128_P	0.633	0.45
90_T	140_I	0.631	0.45
61_S	66_T	0.628	0.45
63_G	70_S	0.627	0.44
113_L	150_L	0.626	0.44
67_L	130_S	0.620	0.44
113_L	156_N	0.618	0.43
56_Y	159_R	0.611	0.43
93_G	117_K	0.611	0.43
56_Y	83_V	0.610	0.43
33_L	43_I	0.609	0.43
41_Q	103_N	0.608	0.42
84_G	139_C	0.606	0.42
106_G	109_G	0.605	0.42
115_L	160_V	0.605	0.42
66_T	132_G	0.601	0.42
84_G	90_T	0.592	0.41
70_S	82_A	0.586	0.40
41_Q	47_G	0.586	0.40
60_V	67_L	0.583	0.40
17_A	128_P	0.580	0.40
25_A	78_T	0.580	0.40
123_H	138_G	0.573	0.39
57_H	133_K	0.570	0.39
46_P	51_P	0.567	0.38
26_L	129_A	0.567	0.38
142_M	152_S	0.565	0.38
58_I	97_I	0.565	0.38
33_L	63_G	0.559	0.38
33_L	36_G	0.559	0.38
128_P	143_H	0.555	0.37
13_N	23_T	0.555	0.37
50_D	54_I	0.551	0.37
67_L	148_I	0.546	0.36
127_N	136_S	0.545	0.36
85_K	145_K	0.544	0.36
21_I	31_P	0.543	0.36
76_M	129_A	0.542	0.36
51_P	70_S	0.539	0.36
125_T	128_P	0.537	0.36
128_P	145_K	0.536	0.35
77_K	110_A	0.533	0.35
39_A	105_G	0.532	0.35
50_D	57_H	0.530	0.35
46_P	132_G	0.529	0.35
99_N	116_S	0.528	0.35
82_A	109_G	0.526	0.34
84_G	111_Y	0.524	0.34
18_D	47_G	0.524	0.34
113_L	122_I	0.523	0.34
57_H	159_R	0.523	0.34
150_L	156_N	0.522	0.34
100_R	155_P	0.519	0.34
16_A	42_S	0.515	0.33
101_Q	114_S	0.510	0.33
131_I	135_V	0.510	0.33
82_A	125_T	0.507	0.33
81_I	130_S	0.507	0.33
25_A	143_H	0.505	0.33
24_A	76_M	0.505	0.33
22_S	25_A	0.505	0.33
13_N	28_Q	0.503	0.32
84_G	95_F	0.502	0.32
84_G	120_Y	0.500	0.32

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
4a1kA	2	1	100	0.251	Contact Map
4lzhA	1	0.9573	100	0.269	Contact Map
4xvoA	1	0.9878	100	0.437	Contact Map
4jmnA	1	0.9939	100	0.449	Contact Map
1zatA	1	0.9817	100	0.48	Contact Map
4k73A	1	0.9695	100	0.505	Contact Map
3vypA	1	1	100	0.511	Contact Map
4qtfA	2	0.9878	100	0.513	Contact Map
5bmqA	3	0.9695	100	0.518	Contact Map
4xxtA	1	0.9634	99.9	0.535	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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