YHDL - BACSU - GREMLIN Contacts

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YHDL - Probable anti-sigma-M factor YhdL

UniProt:	O07581	Sequences: MMNEEFKKRFDQYKNGEMSDQEMTAFEEELEKLEVYQELIDSELEDDNDWDLSISPEKQKAILAYGKRKSYLRISVLAVISTLMILPLCTLGSYLYYGMGGKHSTGNEFMETAAVTVALTMPNVLVDTSGLKSQVKLFGMNTEFPLQKQIGTKTAAVGNERVEMFYNKVKAPAVNYYDLEVNKTGHYFTHPSNKSEQTTAKAEKTLSTLPEGTVSEVYLSYDRAYPTKDVYNKFKGYDVSFLWNAIETEKNTNKTASTEPLGYPGKDSKFLAALNTKGKSNGDQFINALKFMSKHEKWAQVISKRKDLNVDNRLDYVEKNGVNVYGSVVTGPTKEIQRMLKNKSVKSANVGEVELWNW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	358 (293)
Sequences:	289 (244)
Seq/√Len:	14.2

BACSU - YHDL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
222_D	225_Y	5.401	1.00
123_N	216_E	4.965	1.00
216_E	351_G	4.505	1.00
148_K	216_E	4.441	1.00
123_N	351_G	3.468	0.99
285_F	289_L	3.259	0.99
123_N	148_K	3.078	0.98
316_Y	320_N	3.036	0.98
234_F	329_V	2.984	0.97
68_R	71_Y	2.913	0.97
191_P	220_S	2.877	0.97
329_V	336_I	2.842	0.96
72_L	296_E	2.761	0.96
215_S	333_T	2.536	0.93
148_K	351_G	2.522	0.93
226_P	229_D	2.502	0.93
216_E	331_G	2.462	0.92
332_P	335_E	2.461	0.92
140_M	164_M	2.324	0.90
119_L	285_F	2.234	0.88
66_G	220_S	2.189	0.87
151_G	335_E	2.001	0.81
243_W	248_T	1.971	0.80
99_M	138_F	1.863	0.76
211_E	334_K	1.862	0.76
148_K	330_T	1.861	0.76
148_K	218_Y	1.859	0.76
218_Y	221_Y	1.858	0.76
331_G	351_G	1.816	0.74
220_S	328_V	1.799	0.73
82_T	86_L	1.755	0.71
148_K	331_G	1.742	0.71
83_L	86_L	1.735	0.71
220_S	247_E	1.735	0.71
221_Y	327_S	1.722	0.70
76_V	80_I	1.710	0.69
188_F	218_Y	1.684	0.68
175_N	343_K	1.678	0.68
84_M	91_L	1.667	0.67
230_V	327_S	1.663	0.67
247_E	328_V	1.658	0.67
234_F	272_A	1.654	0.67
97_Y	209_L	1.643	0.66
208_T	338_R	1.631	0.66
246_I	336_I	1.613	0.65
223_R	229_D	1.611	0.65
81_S	341_K	1.601	0.64
83_L	127_D	1.592	0.64
206_L	228_K	1.577	0.63
168_K	171_A	1.569	0.62
321_G	325_Y	1.560	0.62
166_Y	317_V	1.558	0.62
163_E	294_K	1.540	0.61
326_G	331_G	1.534	0.61
220_S	346_K	1.532	0.61
334_K	337_Q	1.527	0.60
188_F	222_D	1.520	0.60
199_T	346_K	1.519	0.60
221_Y	225_Y	1.510	0.59
261_L	289_L	1.510	0.59
188_F	220_S	1.505	0.59
191_P	346_K	1.481	0.58
77_L	221_Y	1.479	0.58
81_S	108_E	1.461	0.57
99_M	212_G	1.456	0.57
286_I	293_S	1.453	0.56
78_A	341_K	1.443	0.56
263_Y	266_K	1.435	0.55
214_V	333_T	1.434	0.55
326_G	336_I	1.412	0.54
221_Y	348_A	1.411	0.54
233_K	342_N	1.403	0.54
65_Y	168_K	1.391	0.53
264_P	289_L	1.389	0.53
218_Y	245_A	1.365	0.52
148_K	225_Y	1.363	0.51
216_E	225_Y	1.356	0.51
220_S	336_I	1.349	0.51
290_K	298_W	1.345	0.50
193_N	350_V	1.341	0.50
75_S	85_I	1.337	0.50
65_Y	94_Y	1.337	0.50
334_K	345_V	1.324	0.49
150_I	214_V	1.321	0.49
218_Y	351_G	1.318	0.49
223_R	233_K	1.313	0.49
83_L	91_L	1.310	0.49
118_A	288_A	1.305	0.48
178_D	336_I	1.297	0.48
89_C	244_N	1.297	0.48
92_G	96_Y	1.295	0.48
220_S	324_V	1.290	0.47
246_I	322_V	1.278	0.47
149_Q	240_S	1.269	0.46
246_I	324_V	1.265	0.46
217_V	289_L	1.246	0.45
314_L	345_V	1.230	0.44
119_L	289_L	1.229	0.44
67_K	148_K	1.225	0.44
247_E	336_I	1.218	0.44
123_N	331_G	1.207	0.43
57_E	83_L	1.195	0.42
245_A	325_Y	1.183	0.42
207_S	294_K	1.168	0.41
169_V	327_S	1.163	0.41
201_K	317_V	1.160	0.40
219_L	254_K	1.147	0.40
216_E	220_S	1.145	0.40
191_P	324_V	1.139	0.39
58_K	207_S	1.137	0.39
186_H	344_S	1.133	0.39
200_A	352_E	1.127	0.39
213_T	350_V	1.126	0.39
67_K	70_S	1.122	0.38
150_I	262_G	1.116	0.38
214_V	332_P	1.112	0.38
122_P	243_W	1.109	0.38
190_H	254_K	1.108	0.38
190_H	325_Y	1.107	0.38
73_R	304_K	1.101	0.37
61_A	207_S	1.095	0.37
209_L	325_Y	1.094	0.37
324_V	346_K	1.094	0.37
316_Y	321_G	1.088	0.37
85_I	91_L	1.085	0.37
219_L	329_V	1.085	0.37
260_P	289_L	1.082	0.36
63_L	220_S	1.080	0.36
69_K	329_V	1.079	0.36
177_Y	246_I	1.074	0.36
232_N	283_D	1.066	0.36
203_E	214_V	1.065	0.36
88_L	329_V	1.064	0.36
268_S	272_A	1.060	0.35
177_Y	189_T	1.059	0.35
191_P	243_W	1.057	0.35
192_S	246_I	1.053	0.35
61_A	283_D	1.047	0.35
61_A	87_P	1.046	0.35
219_L	238_D	1.045	0.35
56_P	158_G	1.036	0.34
327_S	331_G	1.025	0.34
151_G	209_L	1.024	0.34
218_Y	348_A	1.023	0.34
220_S	325_Y	1.023	0.34
124_V	330_T	1.023	0.34
142_T	230_V	1.019	0.33
220_S	351_G	1.017	0.33
249_E	332_P	1.014	0.33
203_E	249_E	1.013	0.33
245_A	321_G	1.012	0.33
239_V	340_L	1.011	0.33
239_V	329_V	1.002	0.32
211_E	217_V	1.001	0.32
76_V	100_G	0.999	0.32
349_N	352_E	0.993	0.32
178_D	239_V	0.991	0.32
122_P	345_V	0.988	0.32
246_I	285_F	0.986	0.32
63_L	160_E	0.983	0.32
55_S	63_L	0.974	0.31
186_H	247_E	0.972	0.31
97_Y	264_P	0.964	0.31
138_F	323_N	0.963	0.31
328_V	351_G	0.962	0.31
289_L	292_M	0.961	0.31
146_L	176_Y	0.959	0.30
74_I	196_E	0.959	0.30
154_T	249_E	0.953	0.30
212_G	332_P	0.949	0.30
245_A	347_S	0.946	0.30
161_R	177_Y	0.944	0.30
284_Q	317_V	0.943	0.30
193_N	219_L	0.942	0.30
136_K	246_I	0.941	0.30
97_Y	245_A	0.931	0.29
146_L	165_F	0.926	0.29
64_A	139_G	0.925	0.29
214_V	330_T	0.925	0.29
166_Y	206_L	0.924	0.29
212_G	330_T	0.923	0.29
213_T	247_E	0.907	0.28
85_I	310_V	0.903	0.28
186_H	199_T	0.899	0.28
55_S	327_S	0.895	0.28
164_M	177_Y	0.895	0.28
225_Y	351_G	0.884	0.27
80_I	279_K	0.883	0.27
93_S	97_Y	0.882	0.27
212_G	334_K	0.882	0.27
206_L	213_T	0.882	0.27
61_A	79_V	0.880	0.27
166_Y	334_K	0.879	0.27
146_L	158_G	0.873	0.27
166_Y	327_S	0.867	0.26
150_I	330_T	0.867	0.26
67_K	71_Y	0.865	0.26
214_V	350_V	0.863	0.26
73_R	294_K	0.863	0.26
92_G	338_R	0.861	0.26
67_K	96_Y	0.856	0.26
99_M	140_M	0.854	0.26
321_G	337_Q	0.849	0.26
186_H	201_K	0.848	0.26
65_Y	74_I	0.844	0.25
112_T	138_F	0.839	0.25
65_Y	134_Q	0.838	0.25
186_H	346_K	0.836	0.25
226_P	283_D	0.833	0.25
238_D	340_L	0.824	0.25
220_S	326_G	0.824	0.25
204_K	329_V	0.823	0.25
82_T	343_K	0.821	0.24
119_L	218_Y	0.818	0.24
310_V	314_L	0.818	0.24
74_I	175_N	0.817	0.24
256_A	259_E	0.817	0.24
123_N	225_Y	0.817	0.24
287_N	350_V	0.814	0.24
57_E	65_Y	0.813	0.24
298_W	303_S	0.807	0.24
135_V	141_N	0.806	0.24
119_L	237_Y	0.806	0.24
148_K	328_V	0.806	0.24
307_D	311_D	0.805	0.24
258_T	261_L	0.803	0.24
190_H	220_S	0.801	0.24
67_K	216_E	0.800	0.24
249_E	313_R	0.798	0.24
118_A	183_K	0.796	0.23
248_T	322_V	0.796	0.23
66_G	299_A	0.792	0.23
151_G	349_N	0.786	0.23
218_Y	317_V	0.780	0.23
195_S	199_T	0.780	0.23
213_T	332_P	0.774	0.23
136_K	140_M	0.773	0.23
298_W	302_I	0.773	0.23
178_D	330_T	0.771	0.22
151_G	332_P	0.767	0.22
69_K	317_V	0.767	0.22
220_S	331_G	0.765	0.22
186_H	329_V	0.764	0.22
64_A	208_T	0.762	0.22
140_M	339_M	0.758	0.22
152_T	184_T	0.757	0.22
188_F	225_Y	0.751	0.22
119_L	244_N	0.749	0.22
193_N	205_T	0.748	0.22
239_V	303_S	0.747	0.22
245_A	250_K	0.743	0.21
220_S	339_M	0.742	0.21
97_Y	218_Y	0.742	0.21
96_Y	295_H	0.740	0.21
292_M	296_E	0.739	0.21
207_S	210_P	0.731	0.21
123_N	328_V	0.729	0.21
73_R	78_A	0.728	0.21
119_L	155_A	0.726	0.21
63_L	322_V	0.726	0.21
148_K	245_A	0.724	0.21
155_A	226_P	0.722	0.21
220_S	286_I	0.709	0.20
140_M	235_K	0.705	0.20
292_M	321_G	0.704	0.20
168_K	175_N	0.702	0.20
195_S	202_A	0.701	0.20
84_M	316_Y	0.696	0.20
219_L	289_L	0.694	0.20
155_A	202_A	0.693	0.20
148_K	262_G	0.691	0.20
255_T	263_Y	0.689	0.20
141_N	206_L	0.689	0.20
292_M	322_V	0.687	0.19
221_Y	285_F	0.687	0.19
82_T	85_I	0.686	0.19
262_G	351_G	0.685	0.19
234_F	336_I	0.683	0.19
64_A	162_V	0.682	0.19
189_T	235_K	0.680	0.19
148_K	209_L	0.678	0.19
135_V	263_Y	0.678	0.19
53_S	200_A	0.676	0.19
322_V	328_V	0.674	0.19
76_V	219_L	0.672	0.19
97_Y	318_E	0.668	0.19
99_M	155_A	0.667	0.19
120_T	336_I	0.664	0.19
123_N	218_Y	0.658	0.18
63_L	336_I	0.657	0.18
119_L	292_M	0.656	0.18
178_D	185_G	0.655	0.18
218_Y	328_V	0.655	0.18
245_A	328_V	0.654	0.18
64_A	78_A	0.654	0.18
148_K	220_S	0.652	0.18
94_Y	279_K	0.649	0.18
69_K	201_K	0.648	0.18
158_G	178_D	0.648	0.18
155_A	184_T	0.644	0.18
260_P	348_A	0.643	0.18
200_A	349_N	0.642	0.18
210_P	296_E	0.642	0.18
75_S	82_T	0.642	0.18
202_A	232_N	0.640	0.18
186_H	350_V	0.639	0.18
71_Y	322_V	0.638	0.18
75_S	78_A	0.638	0.18
260_P	285_F	0.638	0.18
247_E	324_V	0.636	0.18
153_K	186_H	0.636	0.18
64_A	207_S	0.636	0.18
117_V	146_L	0.635	0.18
203_E	349_N	0.634	0.18
72_L	80_I	0.631	0.18
98_G	101_G	0.629	0.18
239_V	290_K	0.629	0.18
151_G	240_S	0.628	0.18
140_M	347_S	0.626	0.17
184_T	218_Y	0.625	0.17
202_A	245_A	0.625	0.17
146_L	335_E	0.623	0.17
140_M	245_A	0.621	0.17
184_T	332_P	0.621	0.17
77_L	152_T	0.619	0.17
75_S	89_C	0.617	0.17
314_L	321_G	0.617	0.17
140_M	148_K	0.616	0.17
164_M	202_A	0.616	0.17
239_V	262_G	0.611	0.17
127_D	246_I	0.611	0.17
97_Y	140_M	0.607	0.17
230_V	274_L	0.605	0.17
249_E	325_Y	0.604	0.17
151_G	166_Y	0.601	0.17
279_K	294_K	0.600	0.17
203_E	215_S	0.599	0.17
79_V	311_D	0.596	0.17
211_E	333_T	0.596	0.17
84_M	160_E	0.593	0.16
245_A	332_P	0.593	0.16
188_F	326_G	0.592	0.16
230_V	324_V	0.592	0.16
56_P	83_L	0.592	0.16
99_M	351_G	0.591	0.16
58_K	340_L	0.590	0.16
228_K	297_K	0.589	0.16
135_V	286_I	0.588	0.16
115_V	118_A	0.588	0.16
58_K	211_E	0.587	0.16
74_I	83_L	0.586	0.16
138_F	302_I	0.586	0.16
253_N	293_S	0.582	0.16
101_G	294_K	0.582	0.16
268_S	277_K	0.581	0.16
215_S	250_K	0.580	0.16
56_P	150_I	0.580	0.16
246_I	257_S	0.577	0.16
209_L	352_E	0.577	0.16
69_K	91_L	0.574	0.16
230_V	328_V	0.573	0.16
139_G	166_Y	0.570	0.16
158_G	328_V	0.568	0.16
79_V	279_K	0.567	0.16
56_P	88_L	0.566	0.16
209_L	217_V	0.564	0.16
111_E	217_V	0.564	0.16
114_A	293_S	0.563	0.16
169_V	318_E	0.563	0.16
171_A	283_D	0.562	0.16
69_K	86_L	0.562	0.16
311_D	315_D	0.559	0.15
221_Y	271_L	0.558	0.15
320_N	338_R	0.558	0.15
97_Y	289_L	0.558	0.15
96_Y	299_A	0.557	0.15
213_T	337_Q	0.557	0.15
238_D	302_I	0.555	0.15
168_K	173_A	0.552	0.15
332_P	352_E	0.552	0.15
52_L	184_T	0.551	0.15
234_F	241_F	0.551	0.15
156_A	277_K	0.550	0.15
90_T	119_L	0.549	0.15
128_T	251_N	0.548	0.15
166_Y	284_Q	0.547	0.15
151_G	190_H	0.546	0.15
177_Y	226_P	0.545	0.15
122_P	180_E	0.544	0.15
118_A	289_L	0.543	0.15
123_N	188_F	0.542	0.15
216_E	328_V	0.539	0.15
259_E	303_S	0.539	0.15
186_H	348_A	0.537	0.15
194_K	323_N	0.537	0.15
267_D	318_E	0.537	0.15
70_S	180_E	0.537	0.15
78_A	256_A	0.537	0.15
228_K	251_N	0.536	0.15
264_P	267_D	0.536	0.15
190_H	346_K	0.535	0.15
288_A	321_G	0.534	0.15
148_K	184_T	0.534	0.15
221_Y	245_A	0.534	0.15
177_Y	235_K	0.533	0.15
202_A	221_Y	0.533	0.15
135_V	325_Y	0.529	0.15
93_S	96_Y	0.529	0.15
192_S	289_L	0.528	0.15
141_N	186_H	0.528	0.15
62_I	211_E	0.526	0.15
210_P	262_G	0.526	0.15
97_Y	100_G	0.526	0.15
240_S	244_N	0.524	0.14
147_Q	235_K	0.519	0.14
294_K	320_N	0.519	0.14
235_K	339_M	0.518	0.14
227_T	282_G	0.517	0.14
300_Q	323_N	0.517	0.14
88_L	170_K	0.514	0.14
242_L	263_Y	0.513	0.14
63_L	329_V	0.512	0.14
215_S	332_P	0.512	0.14
243_W	345_V	0.510	0.14
95_L	158_G	0.510	0.14
219_L	327_S	0.510	0.14
238_D	317_V	0.509	0.14
153_K	247_E	0.508	0.14
177_Y	203_E	0.507	0.14
242_L	324_V	0.507	0.14
230_V	322_V	0.507	0.14
83_L	118_A	0.506	0.14
317_V	321_G	0.504	0.14
227_T	287_N	0.504	0.14
80_I	255_T	0.503	0.14
74_I	291_F	0.503	0.14
207_S	337_Q	0.503	0.14
171_A	345_V	0.502	0.14
203_E	217_V	0.500	0.14
69_K	217_V	0.500	0.14

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
3hugB	2	0.1425	96.4	0.927	Contact Map
4nqwB	1	0.1788	93.9	0.938	Contact Map
2kogA	1	0.1872	89.1	0.946	Contact Map
3hd7A	1	0.2235	64	0.957	Contact Map
2m8rA	1	0.2598	50.9	0.96	Contact Map
2q1zB	1	0.4888	49.2	0.961	Contact Map
4kqtA	1	0.3212	32.4	0.965	Contact Map
1u2mA	3	0.2765	24.7	0.967	Contact Map
4jioA	1	0.3073	20.4	0.968	Contact Map
3p0jA	1	0.1704	20.4	0.968	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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