ERFK - ECOLI - GREMLIN Contacts

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ERFK - Probable L,D-transpeptidase ErfK/SrfK

UniProt:	P39176	Sequences: MRRVNILCSFALLFASHTSLAVTYPLPPEGSRLVGQSFTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQLILPDTVRKGIVVNVAEMRLYYYPPDSNTVEVFPIGIGQAGRETPRNWVTTVERKQEAPTWTPTPNTRREYAKRGESLPAFVPAGPDNPMGLYAIYIGRLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVGTRVQIIDQPVKYTTEPDGSNWLEVHEPLSRNRAEYESDRKVPLPVTPSLRAFINGQEVDVNRANAALQRRSGMPVQISSGSRQMF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12682
Length:	310 (289)
Sequences:	560 (348)
Seq/√Len:	20.5

ECOLI - ERFK YBIS YCFS YNHG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_T	231_I	4.978	1.00
137_T	185_G	4.730	1.00
141_R	183_Y	4.562	1.00
104_E	236_K	4.275	1.00
128_G	204_S	4.215	1.00
157_E	205_Q	3.922	1.00
152_P	156_R	3.733	1.00
108_Y	236_K	3.464	1.00
177_M	189_A	3.379	1.00
104_E	108_Y	3.030	0.99
247_L	288_A	2.941	0.99
120_F	217_Y	2.620	0.98
88_L	119_V	2.599	0.98
129_R	205_Q	2.554	0.98
123_G	204_S	2.450	0.97
155_R	167_A	2.421	0.97
149_T	171_A	2.365	0.96
212_N	216_K	2.281	0.96
89_I	238_T	2.259	0.95
239_T	245_N	2.248	0.95
55_A	64_M	2.247	0.95
93_T	110_Y	2.247	0.95
183_Y	189_A	2.212	0.95
149_T	168_F	2.190	0.95
64_M	82_L	2.101	0.93
102_V	184_I	2.067	0.93
156_R	160_K	2.061	0.93
158_Y	163_E	2.059	0.92
147_T	171_A	2.041	0.92
199_I	203_V	2.009	0.92
198_G	203_V	2.002	0.91
248_E	299_P	1.992	0.91
159_A	164_S	1.988	0.91
139_V	182_I	1.945	0.90
181_A	215_I	1.892	0.89
127_A	204_S	1.889	0.89
32_R	238_T	1.879	0.88
55_A	213_D	1.859	0.88
154_T	205_Q	1.853	0.88
209_R	236_K	1.852	0.88
19_S	34_V	1.846	0.88
108_Y	231_I	1.810	0.87
122_I	208_I	1.783	0.86
72_D	75_L	1.750	0.85
45_H	77_K	1.741	0.84
145_A	179_L	1.735	0.84
60_G	198_G	1.735	0.84
40_V	57_Y	1.698	0.83
151_T	154_T	1.692	0.82
181_A	189_A	1.674	0.82
55_A	196_N	1.668	0.82
33_L	89_I	1.641	0.80
100_V	208_I	1.630	0.80
247_L	302_I	1.610	0.79
153_N	205_Q	1.599	0.79
14_F	18_T	1.578	0.78
72_D	197_F	1.551	0.76
285_V	288_A	1.542	0.76
54_A	64_M	1.541	0.76
136_V	227_R	1.523	0.75
247_L	291_A	1.515	0.75
283_V	288_A	1.493	0.74
232_D	253_L	1.475	0.73
45_H	78_S	1.471	0.72
123_G	128_G	1.453	0.72
126_Q	157_E	1.436	0.71
129_R	134_N	1.431	0.70
153_N	187_L	1.423	0.70
150_P	155_R	1.412	0.69
42_V	45_H	1.407	0.69
13_L	20_L	1.397	0.68
136_V	229_Q	1.390	0.68
288_A	302_I	1.378	0.67
151_T	187_L	1.376	0.67
60_G	72_D	1.375	0.67
9_S	14_F	1.374	0.67
190_I	210_L	1.359	0.66
51_E	211_R	1.352	0.66
248_E	295_R	1.342	0.65
180_Y	220_D	1.312	0.63
120_F	189_A	1.302	0.63
129_R	157_E	1.298	0.63
71_A	76_P	1.298	0.63
93_T	233_Q	1.296	0.62
55_A	211_R	1.283	0.62
196_N	199_I	1.270	0.61
102_V	230_I	1.257	0.60
200_G	228_V	1.244	0.59
73_V	128_G	1.237	0.59
96_K	113_D	1.223	0.58
198_G	201_L	1.218	0.58
34_V	88_L	1.213	0.57
145_A	225_G	1.207	0.57
85_P	106_R	1.206	0.57
75_L	197_F	1.205	0.57
33_L	87_Q	1.201	0.56
98_I	139_V	1.199	0.56
60_G	69_P	1.198	0.56
45_H	177_M	1.185	0.55
184_I	189_A	1.184	0.55
239_T	243_G	1.179	0.55
244_S	301_Q	1.176	0.55
9_S	15_A	1.157	0.54
71_A	80_S	1.151	0.53
150_P	209_R	1.147	0.53
249_V	291_A	1.146	0.53
81_Q	110_Y	1.139	0.52
52_T	74_F	1.131	0.52
143_Q	224_V	1.126	0.52
235_V	285_V	1.124	0.51
50_L	64_M	1.123	0.51
182_I	216_K	1.122	0.51
216_K	220_D	1.120	0.51
150_P	188_Y	1.118	0.51
131_T	208_I	1.114	0.51
184_I	188_Y	1.107	0.50
289_N	292_L	1.104	0.50
179_L	212_N	1.104	0.50
160_K	168_F	1.103	0.50
51_E	55_A	1.102	0.50
150_P	236_K	1.091	0.49
63_N	201_L	1.086	0.49
10_F	159_A	1.076	0.48
89_I	260_Y	1.070	0.48
138_T	224_V	1.065	0.48
33_L	246_W	1.061	0.47
224_V	284_D	1.061	0.47
290_A	294_R	1.056	0.47
63_N	238_T	1.049	0.47
107_L	194_N	1.040	0.46
42_V	77_K	1.039	0.46
105_M	204_S	1.038	0.46
70_G	300_V	1.036	0.46
250_H	299_P	1.032	0.45
104_E	209_R	1.031	0.45
37_S	122_I	1.031	0.45
32_R	65_L	1.025	0.45
113_D	139_V	1.021	0.45
223_P	226_T	1.011	0.44
182_I	246_W	1.010	0.44
92_D	233_Q	0.998	0.43
54_A	211_R	0.994	0.43
184_I	212_N	0.993	0.43
203_V	299_P	0.984	0.42
63_N	302_I	0.978	0.42
125_G	297_G	0.976	0.42
159_A	300_V	0.976	0.42
27_P	253_L	0.971	0.41
236_K	248_E	0.971	0.41
105_M	143_Q	0.969	0.41
158_Y	197_F	0.968	0.41
42_V	78_S	0.963	0.41
71_A	103_A	0.962	0.41
95_R	189_A	0.962	0.41
284_D	290_A	0.956	0.41
66_E	251_E	0.950	0.40
28_P	144_E	0.941	0.40
124_I	128_G	0.940	0.40
9_S	17_H	0.933	0.39
138_T	225_G	0.931	0.39
125_G	209_R	0.930	0.39
49_P	74_F	0.929	0.39
291_A	300_V	0.925	0.39
84_I	230_I	0.924	0.39
15_A	18_T	0.918	0.38
125_G	188_Y	0.914	0.38
34_V	263_D	0.908	0.38
33_L	238_T	0.904	0.37
158_Y	195_A	0.900	0.37
250_H	295_R	0.899	0.37
42_V	79_G	0.895	0.37
174_D	216_K	0.894	0.37
67_A	85_P	0.891	0.36
19_S	28_P	0.891	0.36
39_T	81_Q	0.889	0.36
167_A	284_D	0.883	0.36
77_K	80_S	0.880	0.36
61_L	140_E	0.877	0.36
152_P	167_A	0.877	0.36
84_I	219_F	0.876	0.36
73_V	302_I	0.873	0.35
34_V	180_Y	0.870	0.35
53_F	221_N	0.868	0.35
134_N	196_N	0.865	0.35
28_P	95_R	0.861	0.35
61_L	73_V	0.859	0.35
102_V	145_A	0.859	0.35
62_S	73_V	0.855	0.34
53_F	154_T	0.851	0.34
48_Q	177_M	0.837	0.33
110_Y	270_V	0.836	0.33
73_V	123_G	0.831	0.33
129_R	187_L	0.828	0.33
26_L	111_P	0.825	0.33
38_F	86_Q	0.822	0.32
199_I	249_V	0.821	0.32
99_V	170_P	0.821	0.32
137_T	253_L	0.820	0.32
132_P	162_G	0.816	0.32
108_Y	210_L	0.816	0.32
107_L	243_G	0.812	0.32
109_Y	226_T	0.809	0.32
143_Q	183_Y	0.806	0.31
60_G	106_R	0.806	0.31
248_E	297_G	0.805	0.31
192_G	218_L	0.798	0.31
131_T	196_N	0.797	0.31
156_R	283_V	0.796	0.31
156_R	291_A	0.793	0.31
136_V	225_G	0.792	0.31
9_S	224_V	0.791	0.31
103_A	266_V	0.790	0.31
165_L	184_I	0.785	0.30
105_M	205_Q	0.781	0.30
276_A	287_R	0.781	0.30
110_Y	118_E	0.779	0.30
31_S	199_I	0.777	0.30
17_H	20_L	0.776	0.30
49_P	78_S	0.773	0.30
147_T	168_F	0.771	0.30
91_P	175_N	0.770	0.29
145_A	180_Y	0.769	0.29
90_L	117_V	0.766	0.29
140_E	183_Y	0.762	0.29
134_N	212_N	0.761	0.29
169_V	230_I	0.761	0.29
232_D	252_P	0.755	0.29
155_R	165_L	0.755	0.29
167_A	223_P	0.754	0.29
30_G	37_S	0.751	0.28
10_F	18_T	0.750	0.28
98_I	222_V	0.748	0.28
186_R	230_I	0.746	0.28
71_A	75_L	0.744	0.28
62_S	102_V	0.743	0.28
12_L	15_A	0.731	0.27
177_M	199_I	0.726	0.27
69_P	210_L	0.718	0.27
90_L	199_I	0.716	0.27
12_L	20_L	0.715	0.27
10_F	16_S	0.714	0.27
90_L	97_G	0.714	0.27
157_E	203_V	0.712	0.26
130_E	194_N	0.712	0.26
100_V	230_I	0.712	0.26
49_P	126_Q	0.711	0.26
105_M	183_Y	0.711	0.26
168_F	171_A	0.707	0.26
170_P	209_R	0.706	0.26
58_G	283_V	0.703	0.26
34_V	224_V	0.699	0.26
27_P	111_P	0.699	0.26
60_G	85_P	0.696	0.26
180_Y	215_I	0.696	0.26
155_R	209_R	0.690	0.25
23_T	40_V	0.689	0.25
210_L	288_A	0.688	0.25
26_L	94_V	0.684	0.25
238_T	255_R	0.683	0.25
67_A	183_Y	0.680	0.25
39_T	292_L	0.678	0.25
15_A	159_A	0.677	0.25
110_Y	231_I	0.675	0.25
250_H	297_G	0.672	0.24
131_T	216_K	0.672	0.24
118_E	217_Y	0.671	0.24
63_N	158_Y	0.660	0.24
29_E	95_R	0.660	0.24
52_T	163_E	0.657	0.24
110_Y	185_G	0.656	0.24
249_V	301_Q	0.654	0.24
235_V	275_R	0.654	0.24
61_L	192_G	0.652	0.23
11_A	16_S	0.652	0.23
17_H	21_A	0.651	0.23
199_I	204_S	0.651	0.23
216_K	253_L	0.648	0.23
123_G	127_A	0.648	0.23
104_E	150_P	0.648	0.23
189_A	201_L	0.646	0.23
102_V	194_N	0.645	0.23
68_N	97_G	0.645	0.23
161_R	174_D	0.645	0.23
59_Q	65_L	0.644	0.23
269_P	272_P	0.644	0.23
153_N	157_E	0.642	0.23
182_I	219_F	0.640	0.23
150_P	197_F	0.639	0.23
113_D	219_F	0.638	0.23
54_A	199_I	0.637	0.23
159_A	169_V	0.636	0.23
10_F	17_H	0.636	0.23
180_Y	216_K	0.634	0.23
126_Q	129_R	0.632	0.23
100_V	263_D	0.630	0.22
33_L	42_V	0.629	0.22
59_Q	64_M	0.629	0.22
43_P	110_Y	0.627	0.22
76_P	85_P	0.627	0.22
104_E	248_E	0.625	0.22
15_A	19_S	0.624	0.22
133_R	138_T	0.624	0.22
33_L	80_S	0.622	0.22
13_L	17_H	0.621	0.22
31_S	241_P	0.616	0.22
249_V	292_L	0.614	0.22
86_Q	156_R	0.613	0.22
202_R	243_G	0.611	0.22
172_G	176_P	0.611	0.22
32_R	122_I	0.610	0.22
249_V	273_S	0.608	0.21
158_Y	164_S	0.607	0.21
22_V	86_Q	0.604	0.21
141_R	187_L	0.604	0.21
49_P	177_M	0.603	0.21
204_S	254_S	0.603	0.21
51_E	74_F	0.603	0.21
142_K	226_T	0.603	0.21
62_S	105_M	0.601	0.21
202_R	232_D	0.601	0.21
12_L	16_S	0.600	0.21
34_V	119_V	0.598	0.21
10_F	275_R	0.597	0.21
184_I	208_I	0.593	0.21
48_Q	284_D	0.592	0.21
195_A	203_V	0.592	0.21
138_T	227_R	0.591	0.21
18_T	56_Q	0.591	0.21
73_V	204_S	0.590	0.21
48_Q	285_V	0.590	0.21
41_T	287_R	0.589	0.21
264_R	274_L	0.583	0.20
144_E	237_Y	0.583	0.20
151_T	186_R	0.583	0.20
106_R	200_G	0.580	0.20
14_F	17_H	0.578	0.20
243_G	254_S	0.576	0.20
158_Y	198_G	0.575	0.20
235_V	249_V	0.574	0.20
150_P	210_L	0.573	0.20
158_Y	165_L	0.572	0.20
61_L	198_G	0.572	0.20
63_N	119_V	0.570	0.20
62_S	196_N	0.569	0.20
74_F	129_R	0.568	0.20
49_P	52_T	0.567	0.20
143_Q	230_I	0.567	0.20
139_V	145_A	0.566	0.20
58_G	230_I	0.566	0.20
84_I	250_H	0.565	0.20
165_L	203_V	0.564	0.20
90_L	111_P	0.564	0.20
138_T	296_S	0.563	0.20
173_P	225_G	0.563	0.20
95_R	150_P	0.561	0.19
125_G	184_I	0.561	0.19
165_L	248_E	0.560	0.19
199_I	213_D	0.560	0.19
165_L	299_P	0.557	0.19
140_E	153_N	0.556	0.19
108_Y	150_P	0.556	0.19
32_R	95_R	0.553	0.19
203_V	291_A	0.552	0.19
90_L	110_Y	0.551	0.19
114_S	141_R	0.549	0.19
66_E	75_L	0.549	0.19
73_V	84_I	0.548	0.19
166_P	189_A	0.546	0.19
39_T	164_S	0.546	0.19
67_A	226_T	0.546	0.19
18_T	302_I	0.545	0.19
49_P	59_Q	0.544	0.19
44_D	77_K	0.543	0.19
131_T	193_T	0.542	0.19
107_L	202_R	0.541	0.19
217_Y	221_N	0.540	0.19
12_L	17_H	0.539	0.19
224_V	293_Q	0.538	0.19
195_A	295_R	0.538	0.19
270_V	275_R	0.537	0.18
84_I	217_Y	0.537	0.18
157_E	296_S	0.536	0.18
155_R	236_K	0.534	0.18
270_V	292_L	0.534	0.18
142_K	234_P	0.533	0.18
53_F	199_I	0.532	0.18
101_N	125_G	0.531	0.18
55_A	134_N	0.531	0.18
193_T	212_N	0.530	0.18
210_L	215_I	0.529	0.18
245_N	287_R	0.528	0.18
100_V	218_L	0.528	0.18
196_N	212_N	0.527	0.18
239_T	281_Q	0.527	0.18
100_V	130_E	0.525	0.18
84_I	197_F	0.525	0.18
89_I	116_T	0.525	0.18
26_L	117_V	0.524	0.18
142_K	218_L	0.523	0.18
188_Y	297_G	0.522	0.18
140_E	184_I	0.522	0.18
103_A	192_G	0.521	0.18
105_M	155_R	0.521	0.18
162_G	201_L	0.520	0.18
101_N	297_G	0.520	0.18
10_F	272_P	0.518	0.18
222_V	226_T	0.518	0.18
25_P	113_D	0.515	0.18
9_S	13_L	0.514	0.18
16_S	20_L	0.514	0.18
105_M	189_A	0.513	0.18
55_A	212_N	0.513	0.18
31_S	103_A	0.512	0.18
126_Q	245_N	0.512	0.18
211_R	233_Q	0.510	0.17
90_L	152_P	0.508	0.17
94_V	111_P	0.508	0.17
45_H	74_F	0.505	0.17
121_P	243_G	0.505	0.17
70_G	76_P	0.505	0.17
26_L	288_A	0.504	0.17
182_I	215_I	0.503	0.17
123_G	192_G	0.503	0.17
293_Q	302_I	0.503	0.17
273_S	277_F	0.502	0.17
104_E	215_I	0.502	0.17
40_V	89_I	0.502	0.17
142_K	224_V	0.502	0.17
139_V	258_A	0.502	0.17
151_T	177_M	0.501	0.17
125_G	215_I	0.501	0.17
13_L	274_L	0.500	0.17
121_P	214_D	0.500	0.17
90_L	109_Y	0.500	0.17

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
4lzhA	1	0.8871	100	0.399	Contact Map
4xvoA	1	0.6323	100	0.662	Contact Map
4jmnA	1	0.6323	100	0.664	Contact Map
4a1kA	2	0.529	100	0.681	Contact Map
4k73A	1	0.6065	100	0.737	Contact Map
3vypA	1	0.7387	100	0.751	Contact Map
1zatA	1	0.6645	100	0.761	Contact Map
4qtfA	2	0.7581	100	0.762	Contact Map
5bmqA	3	0.5871	100	0.767	Contact Map
4xxtA	1	0.5903	100	0.779	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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