YCFS - ECOLI - GREMLIN Contacts

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YCFS - Probable L,D-transpeptidase YcfS

UniProt:	P75954	Sequences: MMIKTRFSRWLTFFTFAAAVALALPAKANTWPLPPAGSRLVGENKFHVVENDGGSLEAIAKKYNVGFLALLQANPGVDPYVPRAGSVLTIPLQTLLPDAPREGIVINIAELRLYYYPPGKNSVTVYPIGIGQLGGDTLTPTMVTTVSDKRANPTWTPTANIRARYKAQGIELPAVVPAGLDNPMGHHAIRLAAYGGVYLLHGTNADFGIGMRVSSGCIRLRDDDIKTLFSQVTPGTKVNIINTPIKVSAEPNGARLVEVHQPLSEKIDDDPQLLPITLNSAMQSFKDAAQTDAEVMQHVMDVRSGMPVDVRRHQVSPQTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13437
Length:	320 (293)
Sequences:	559 (344)
Seq/√Len:	20.1

ECOLI - YCFS YBIS YNHG ERFK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_A	241_I	5.633	1.00
144_T	192_A	5.133	1.00
148_D	190_R	4.867	1.00
134_G	214_S	4.448	1.00
110_E	246_K	4.404	1.00
159_A	163_A	3.993	1.00
114_Y	246_K	3.594	1.00
184_M	199_L	3.511	1.00
164_R	215_S	3.434	1.00
257_V	296_M	3.324	1.00
110_E	114_Y	3.176	1.00
95_L	248_S	2.675	0.98
129_G	214_S	2.636	0.98
126_Y	227_T	2.582	0.98
94_T	125_V	2.550	0.98
26_A	41_V	2.542	0.98
135_G	215_S	2.463	0.97
222_D	226_K	2.394	0.97
156_T	178_A	2.381	0.96
61_K	70_L	2.378	0.96
162_R	174_A	2.342	0.96
156_T	175_V	2.290	0.96
208_G	213_V	2.289	0.96
219_R	246_K	2.245	0.95
99_A	116_Y	2.240	0.95
161_I	215_S	2.160	0.94
154_T	178_A	2.089	0.93
190_R	199_L	2.070	0.92
108_I	191_L	2.012	0.91
249_A	255_R	1.986	0.91
128_I	218_I	1.959	0.90
61_K	223_D	1.946	0.90
60_A	70_L	1.944	0.90
188_A	225_I	1.943	0.90
53_G	83_R	1.916	0.89
209_I	213_V	1.908	0.89
70_L	88_L	1.898	0.89
133_L	214_S	1.848	0.87
146_V	189_I	1.843	0.87
61_K	206_D	1.830	0.87
257_V	310_V	1.830	0.87
152_N	186_H	1.803	0.86
258_E	307_P	1.801	0.86
257_V	299_V	1.799	0.86
158_T	161_I	1.784	0.85
78_D	81_V	1.781	0.85
49_V	53_G	1.781	0.85
165_Y	170_I	1.775	0.85
114_Y	241_I	1.775	0.85
106_I	218_I	1.746	0.84
66_G	208_G	1.733	0.83
157_P	162_R	1.658	0.81
291_T	296_M	1.634	0.80
142_M	193_A	1.605	0.78
47_H	63_Y	1.601	0.78
20_V	27_K	1.594	0.78
160_N	215_S	1.583	0.77
78_D	207_F	1.576	0.77
39_R	248_S	1.538	0.75
66_G	78_D	1.483	0.72
149_K	192_A	1.476	0.72
188_A	199_L	1.464	0.71
57_E	221_R	1.450	0.71
166_K	171_E	1.424	0.69
129_G	134_G	1.403	0.68
35_P	101_R	1.400	0.68
132_Q	164_R	1.382	0.67
79_P	134_G	1.374	0.66
143_V	239_N	1.368	0.66
163_A	167_A	1.366	0.66
87_V	116_Y	1.359	0.65
16_F	22_L	1.358	0.65
187_H	230_S	1.355	0.65
200_L	220_L	1.352	0.65
143_V	237_K	1.343	0.65
110_E	219_R	1.320	0.63
293_A	296_M	1.319	0.63
126_Y	199_L	1.310	0.63
226_K	230_S	1.306	0.62
54_G	184_M	1.304	0.62
135_G	164_R	1.290	0.61
40_L	95_L	1.287	0.61
104_I	146_V	1.282	0.61
108_I	240_I	1.277	0.61
191_L	198_Y	1.276	0.60
61_K	221_R	1.275	0.60
53_G	84_A	1.250	0.59
245_I	293_A	1.248	0.59
242_N	263_L	1.242	0.58
206_D	209_I	1.241	0.58
21_A	25_P	1.236	0.58
81_V	207_F	1.235	0.58
41_V	94_T	1.230	0.58
58_A	80_Y	1.217	0.57
208_G	211_M	1.216	0.57
49_V	84_A	1.203	0.56
296_M	310_V	1.202	0.56
157_P	219_R	1.184	0.55
166_K	308_V	1.177	0.54
68_L	79_P	1.173	0.54
150_R	234_P	1.172	0.54
77_V	86_S	1.167	0.54
249_A	253_G	1.149	0.52
210_G	238_V	1.143	0.52
297_Q	300_M	1.133	0.51
113_L	253_G	1.127	0.51
76_G	308_V	1.123	0.51
258_E	303_R	1.111	0.50
145_T	234_P	1.106	0.50
69_A	211_M	1.104	0.49
157_P	198_Y	1.104	0.49
292_D	298_H	1.102	0.49
96_L	209_I	1.097	0.49
135_G	142_M	1.096	0.49
22_L	25_P	1.095	0.49
139_T	218_I	1.093	0.49
157_P	246_K	1.092	0.49
260_H	307_P	1.088	0.48
22_L	26_A	1.084	0.48
159_A	174_A	1.082	0.48
99_A	243_T	1.075	0.48
72_Q	261_Q	1.070	0.47
56_L	70_L	1.069	0.47
189_I	226_K	1.065	0.47
40_L	93_Q	1.061	0.47
165_Y	207_F	1.058	0.46
69_A	248_S	1.055	0.46
98_D	243_T	1.051	0.46
60_A	221_R	1.051	0.46
152_N	235_G	1.040	0.45
111_L	214_S	1.040	0.45
30_T	47_H	1.025	0.44
101_R	199_L	1.019	0.44
114_Y	220_L	1.013	0.44
130_I	134_G	1.005	0.43
233_T	236_T	1.004	0.43
271_P	308_V	1.002	0.43
254_A	309_D	1.002	0.43
67_F	147_S	1.000	0.43
91_P	112_R	0.999	0.43
131_G	219_R	0.984	0.42
259_V	299_V	0.982	0.42
105_V	177_P	0.981	0.42
42_G	241_I	0.976	0.41
49_V	253_G	0.973	0.41
189_I	256_L	0.967	0.41
145_T	235_G	0.966	0.41
191_L	199_L	0.966	0.41
142_M	192_A	0.966	0.41
104_I	232_V	0.965	0.41
112_R	210_G	0.951	0.40
102_E	119_G	0.946	0.39
150_R	190_R	0.943	0.39
16_F	21_A	0.928	0.38
77_V	109_A	0.924	0.38
29_N	64_N	0.922	0.38
147_S	192_A	0.920	0.38
212_R	242_N	0.914	0.37
299_V	308_V	0.913	0.37
57_E	61_K	0.893	0.36
186_H	222_D	0.891	0.36
49_V	85_G	0.889	0.36
277_T	281_A	0.885	0.36
164_R	170_I	0.884	0.36
152_N	187_H	0.876	0.35
46_F	87_V	0.873	0.35
19_A	27_K	0.865	0.34
116_Y	241_I	0.864	0.34
77_V	82_P	0.859	0.34
147_S	190_R	0.859	0.34
167_A	175_V	0.857	0.34
83_R	86_S	0.857	0.34
248_S	265_E	0.855	0.34
131_G	198_Y	0.849	0.33
181_D	226_K	0.847	0.33
298_H	302_V	0.842	0.33
69_A	310_V	0.842	0.33
269_D	274_L	0.841	0.33
143_V	235_G	0.840	0.33
162_R	219_R	0.838	0.33
246_K	258_E	0.837	0.33
131_G	305_G	0.837	0.33
90_I	229_F	0.835	0.33
177_P	219_R	0.834	0.33
73_A	236_T	0.834	0.33
119_G	279_N	0.831	0.32
21_A	24_L	0.830	0.32
59_I	231_Q	0.829	0.32
162_R	172_L	0.827	0.32
55_S	84_A	0.826	0.32
45_K	92_L	0.826	0.32
40_L	256_L	0.824	0.32
175_V	178_A	0.822	0.32
144_T	263_L	0.821	0.32
209_I	214_S	0.816	0.32
135_G	195_G	0.814	0.31
174_A	292_D	0.813	0.31
165_Y	205_A	0.810	0.31
49_V	83_R	0.809	0.31
91_P	210_G	0.809	0.31
220_L	296_M	0.803	0.31
213_V	307_P	0.802	0.31
140_P	169_G	0.799	0.31
116_Y	192_A	0.797	0.31
33_L	37_G	0.797	0.31
73_A	91_P	0.796	0.30
100_P	117_P	0.790	0.30
16_F	24_L	0.790	0.30
54_G	59_I	0.788	0.30
16_F	20_V	0.786	0.30
15_T	18_A	0.784	0.30
242_N	262_P	0.781	0.30
90_I	240_I	0.781	0.30
80_Y	135_G	0.780	0.30
146_V	152_N	0.777	0.29
56_L	128_I	0.776	0.29
24_L	28_A	0.773	0.29
209_I	259_V	0.772	0.29
295_V	299_V	0.771	0.29
82_P	85_G	0.766	0.29
139_T	226_K	0.759	0.28
79_P	129_G	0.756	0.28
234_P	292_D	0.755	0.28
14_F	18_A	0.753	0.28
163_A	291_T	0.749	0.28
33_L	117_P	0.748	0.28
96_L	103_G	0.748	0.28
110_E	157_P	0.748	0.28
66_G	112_R	0.747	0.28
142_M	222_D	0.747	0.28
111_L	150_R	0.746	0.28
73_A	190_R	0.746	0.28
172_L	213_V	0.745	0.28
109_A	129_G	0.743	0.28
44_N	128_I	0.742	0.28
120_K	257_V	0.739	0.27
68_L	108_I	0.738	0.27
64_N	291_T	0.735	0.27
66_G	75_P	0.733	0.27
195_G	240_I	0.731	0.27
163_A	299_V	0.730	0.27
115_Y	236_T	0.721	0.27
255_R	295_V	0.715	0.26
240_I	292_D	0.714	0.26
80_Y	211_M	0.709	0.26
41_V	109_A	0.708	0.26
260_H	303_R	0.707	0.26
253_G	264_S	0.704	0.26
195_G	215_S	0.702	0.26
20_V	26_A	0.700	0.25
19_A	23_A	0.700	0.25
50_E	53_G	0.698	0.25
184_M	209_I	0.697	0.25
206_D	222_D	0.696	0.25
110_E	225_I	0.693	0.25
52_D	83_R	0.691	0.25
226_K	263_L	0.689	0.25
129_G	202_G	0.688	0.25
172_L	191_L	0.687	0.25
142_M	206_D	0.686	0.25
67_F	202_G	0.685	0.25
172_L	258_E	0.684	0.25
157_P	207_F	0.683	0.25
119_G	229_F	0.682	0.25
66_G	80_Y	0.681	0.25
157_P	220_L	0.680	0.24
113_L	204_N	0.680	0.24
112_R	238_V	0.679	0.24
131_G	225_I	0.678	0.24
59_I	161_I	0.678	0.24
66_G	210_G	0.676	0.24
160_N	164_R	0.676	0.24
60_A	209_I	0.672	0.24
258_E	299_V	0.672	0.24
129_G	133_L	0.670	0.24
67_F	79_P	0.669	0.24
212_R	253_G	0.668	0.24
273_L	310_V	0.668	0.24
124_T	227_T	0.666	0.24
79_P	214_S	0.665	0.24
165_Y	208_G	0.662	0.24
17_A	23_A	0.661	0.24
101_R	157_P	0.659	0.24
82_P	91_P	0.658	0.23
164_R	168_Q	0.658	0.23
14_F	21_A	0.655	0.23
24_L	27_K	0.654	0.23
111_L	215_S	0.654	0.23
145_T	237_K	0.652	0.23
77_V	81_V	0.652	0.23
189_I	229_F	0.650	0.23
95_L	122_S	0.648	0.23
19_A	241_I	0.648	0.23
14_F	19_A	0.648	0.23
90_I	187_H	0.645	0.23
259_V	309_D	0.645	0.23
191_L	222_D	0.643	0.23
96_L	159_A	0.642	0.23
131_G	191_L	0.637	0.22
71_L	157_P	0.634	0.22
169_G	211_M	0.634	0.22
92_L	163_A	0.633	0.22
168_Q	181_D	0.632	0.22
158_T	184_M	0.629	0.22
121_N	259_V	0.627	0.22
166_K	176_V	0.626	0.22
139_T	206_D	0.625	0.22
34_P	117_P	0.624	0.22
142_M	199_L	0.624	0.22
90_I	260_H	0.620	0.22
65_V	71_L	0.617	0.22
123_V	169_G	0.617	0.22
58_A	170_I	0.617	0.22
116_Y	124_T	0.616	0.22
166_K	247_V	0.616	0.22
205_A	213_V	0.614	0.21
113_L	212_R	0.612	0.21
69_A	165_Y	0.609	0.21
198_Y	305_G	0.607	0.21
30_T	37_G	0.607	0.21
146_V	268_D	0.606	0.21
162_R	246_K	0.605	0.21
37_G	41_V	0.604	0.21
191_L	202_G	0.602	0.21
90_I	207_F	0.601	0.21
17_A	24_L	0.598	0.21
189_I	225_I	0.597	0.21
164_R	211_M	0.597	0.21
42_G	91_P	0.596	0.21
39_R	101_R	0.594	0.21
31_W	41_V	0.592	0.21
75_P	112_R	0.592	0.21
66_G	91_P	0.590	0.20
26_A	279_N	0.588	0.20
191_L	225_I	0.587	0.20
74_N	173_P	0.586	0.20
161_I	261_Q	0.584	0.20
41_V	187_H	0.584	0.20
44_N	95_L	0.583	0.20
103_G	237_K	0.582	0.20
135_G	160_N	0.582	0.20
96_L	116_Y	0.581	0.20
150_R	192_A	0.580	0.20
165_Y	172_L	0.580	0.20
85_G	184_M	0.580	0.20
29_N	291_T	0.577	0.20
55_S	80_Y	0.577	0.20
212_R	263_L	0.576	0.20
154_T	298_H	0.574	0.20
33_L	169_G	0.573	0.20
70_L	188_A	0.572	0.20
108_I	152_N	0.571	0.20
140_P	258_E	0.570	0.20
145_T	220_L	0.569	0.20
61_K	142_M	0.569	0.20
207_F	258_E	0.568	0.20
145_T	304_S	0.566	0.19
67_F	125_V	0.565	0.19
69_A	148_D	0.565	0.19
172_L	187_H	0.564	0.19
203_T	222_D	0.563	0.19
108_I	204_N	0.562	0.19
227_T	302_V	0.562	0.19
25_P	187_H	0.561	0.19
193_A	220_L	0.560	0.19
18_A	21_A	0.560	0.19
184_M	305_G	0.560	0.19
141_T	243_T	0.559	0.19
67_F	208_G	0.558	0.19
180_L	235_G	0.558	0.19
48_V	152_N	0.558	0.19
20_V	282_M	0.556	0.19
107_N	110_E	0.554	0.19
232_V	236_T	0.553	0.19
258_E	305_G	0.553	0.19
281_A	285_F	0.553	0.19
169_G	278_L	0.552	0.19
109_A	202_G	0.551	0.19
176_V	240_I	0.549	0.19
151_A	187_H	0.547	0.19
16_F	48_V	0.544	0.19
103_G	123_V	0.544	0.19
172_L	307_P	0.542	0.18
48_V	295_V	0.542	0.18
40_L	248_S	0.541	0.18
132_Q	255_R	0.541	0.18
41_V	63_Y	0.540	0.18
47_H	54_G	0.540	0.18
65_V	70_L	0.539	0.18
141_T	145_T	0.538	0.18
35_P	151_A	0.538	0.18
66_G	82_P	0.537	0.18
139_T	203_T	0.536	0.18
103_G	117_P	0.535	0.18
30_T	291_T	0.533	0.18
75_P	208_G	0.531	0.18
149_K	228_L	0.531	0.18
47_H	95_L	0.531	0.18
189_I	228_L	0.531	0.18
32_P	35_P	0.530	0.18
36_A	119_G	0.530	0.18
125_V	223_D	0.529	0.18
88_L	158_T	0.528	0.18
133_L	242_N	0.527	0.18
22_L	166_K	0.526	0.18
205_A	303_R	0.525	0.18
160_N	205_A	0.524	0.18
57_E	80_Y	0.524	0.18
136_D	204_N	0.523	0.18
149_K	190_R	0.523	0.18
79_P	310_V	0.523	0.18
32_P	36_A	0.523	0.18
71_L	80_Y	0.523	0.18
170_I	190_R	0.522	0.18
30_T	120_K	0.522	0.18
127_P	253_G	0.521	0.18
119_G	146_V	0.521	0.18
158_T	259_V	0.521	0.18
136_D	209_I	0.518	0.18
53_G	80_Y	0.516	0.17
87_V	243_T	0.516	0.17
47_H	80_Y	0.516	0.17
91_P	238_V	0.515	0.17
168_Q	242_N	0.515	0.17
41_V	125_V	0.515	0.17
199_L	211_M	0.514	0.17
256_L	283_Q	0.513	0.17
247_V	286_K	0.510	0.17
249_A	296_M	0.509	0.17
105_V	171_E	0.509	0.17
33_L	100_P	0.507	0.17
69_A	125_V	0.507	0.17
60_A	257_V	0.506	0.17
173_P	199_L	0.506	0.17
16_F	174_A	0.506	0.17
96_L	115_Y	0.505	0.17
301_D	310_V	0.504	0.17
178_A	187_H	0.504	0.17
15_T	23_A	0.502	0.17
149_K	244_P	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
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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	0.8531	100	0.437	Contact Map
4xvoA	1	0.6156	100	0.68	Contact Map
4jmnA	1	0.6156	100	0.683	Contact Map
4a1kA	2	0.5156	100	0.699	Contact Map
4k73A	1	0.5906	100	0.753	Contact Map
3vypA	1	0.7125	100	0.772	Contact Map
1zatA	1	0.6656	100	0.779	Contact Map
4qtfA	2	0.7625	100	0.781	Contact Map
5bmqA	3	0.5656	100	0.791	Contact Map
4lpqA	1	0.5687	99.9	0.805	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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