BAMB - ECOLI - GREMLIN Contacts

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BAMB - Outer membrane protein assembly factor BamB

UniProt:	P77774	Sequences: MQLRKLLLPGLLSVTLLSGCSLFNSEEDVVKMSPLPTVENQFTPTTAWSTSVGSGIGNFYSNLHPALADNVVYAADRAGLVKALNADDGKEIWSVSLAEKDGWFSKEPALLSGGVTVSGGHVYIGSEKAQVYALNTSDGTVAWQTKVAGEALSRPVVSDGLVLIHTSNGQLQALNEADGAVKWTVNLDMPSLSLRGESAPTTAFGAAVVGGDNGRVSAVLMEQGQMIWQQRISQATGSTEIDRLSDVDTTPVVVNGVVFALAYNGNLTALDLRSGQIMWKRELGSVNDFIVDGNRIYLVDQNDRVMALTIDGGVTLWTQSDLLHRLLTSPVLYNGNLVVGDSEGYLHWINVEDGRFVAQQKVDSSGFQTEPVAADGKLLIQAKDGTVYSITR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14208
Length:	392 (300)
Sequences:	638 (613)
Seq/√Len:	35.4

ECOLI - BAMB
BACSU - YXAL YWHL YWHK
HALSA - Q9HHP3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
323_L	339_V	6.922	1.00
284_G	298_L	5.442	1.00
363_D	381_Q	4.948	1.00
259_F	296_I	3.757	1.00
233_S	260_A	3.587	1.00
210_G	214_G	3.511	1.00
260_A	270_L	3.126	1.00
323_L	343_E	3.121	1.00
209_V	219_V	3.119	1.00
298_L	308_L	3.013	1.00
323_L	327_L	2.962	1.00
302_N	306_M	2.917	1.00
286_V	289_F	2.833	1.00
373_A	376_G	2.654	1.00
284_G	300_D	2.639	1.00
252_V	255_N	2.606	1.00
259_F	269_A	2.605	1.00
123_Y	133_A	2.599	1.00
208_V	251_P	2.523	1.00
297_Y	337_L	2.523	1.00
333_Y	338_V	2.482	1.00
260_A	268_T	2.370	1.00
297_Y	332_L	2.368	1.00
175_N	178_D	2.366	1.00
338_V	372_V	2.359	0.99
323_L	349_I	2.346	0.99
329_S	370_E	2.300	0.99
299_V	327_L	2.286	0.99
305_V	327_L	2.263	0.99
290_I	332_L	2.259	0.99
325_R	341_D	2.185	0.99
85_N	88_D	2.166	0.99
329_S	340_G	2.117	0.99
148_A	164_I	2.110	0.99
267_L	298_L	2.035	0.98
283_L	308_L	2.008	0.98
341_D	345_Y	1.993	0.98
116_T	119_G	1.958	0.98
305_V	339_V	1.942	0.98
220_L	223_Q	1.934	0.98
210_G	246_D	1.924	0.98
284_G	302_N	1.900	0.98
290_I	293_G	1.871	0.97
339_V	349_I	1.866	0.97
300_D	304_R	1.850	0.97
323_L	341_D	1.831	0.97
290_I	297_Y	1.827	0.97
338_V	348_W	1.824	0.97
339_V	343_E	1.788	0.97
372_V	379_L	1.784	0.96
307_A	319_Q	1.766	0.96
209_V	217_S	1.753	0.96
81_V	134_L	1.734	0.96
307_A	317_W	1.718	0.96
123_Y	157_V	1.647	0.94
66_A	73_Y	1.644	0.94
363_D	367_F	1.638	0.94
125_G	129_A	1.628	0.94
269_A	327_L	1.616	0.94
300_D	303_D	1.597	0.93
343_E	347_H	1.593	0.93
168_N	172_Q	1.583	0.93
264_N	268_T	1.542	0.92
204_F	208_V	1.505	0.91
121_H	133_A	1.502	0.91
72_V	75_A	1.463	0.90
67_L	81_V	1.461	0.90
233_S	264_N	1.453	0.90
251_P	258_V	1.416	0.88
159_D	163_L	1.410	0.88
300_D	308_L	1.391	0.88
339_V	347_H	1.380	0.87
117_V	157_V	1.356	0.86
369_T	372_V	1.356	0.86
327_L	339_V	1.345	0.86
362_V	381_Q	1.341	0.86
373_A	380_I	1.334	0.85
333_Y	372_V	1.323	0.85
199_A	210_G	1.305	0.84
296_I	338_V	1.303	0.84
159_D	254_V	1.269	0.82
286_V	298_L	1.248	0.81
135_N	138_D	1.244	0.81
281_R	284_G	1.237	0.81
124_I	134_L	1.224	0.80
264_N	305_V	1.208	0.79
322_L	343_E	1.205	0.79
123_Y	214_G	1.204	0.79
218_A	367_F	1.201	0.79
69_D	81_V	1.198	0.78
332_L	372_V	1.196	0.78
298_L	302_N	1.193	0.78
63_L	66_A	1.182	0.77
118_S	155_P	1.176	0.77
197_E	202_T	1.172	0.77
74_A	124_I	1.171	0.77
323_L	348_W	1.168	0.77
366_G	380_I	1.164	0.76
66_A	216_V	1.161	0.76
331_V	338_V	1.161	0.76
282_E	340_G	1.153	0.76
365_S	380_I	1.149	0.75
288_D	299_V	1.142	0.75
331_V	371_P	1.141	0.75
219_V	308_L	1.130	0.74
208_V	258_V	1.122	0.74
360_Q	381_Q	1.116	0.73
334_N	343_E	1.114	0.73
113_G	118_S	1.113	0.73
163_L	172_Q	1.107	0.73
270_L	346_L	1.101	0.72
68_A	74_A	1.075	0.70
110_L	116_T	1.072	0.70
198_S	202_T	1.068	0.70
298_L	306_M	1.066	0.70
363_D	366_G	1.066	0.70
133_A	178_D	1.055	0.69
374_A	379_L	1.048	0.68
65_P	68_A	1.038	0.68
77_R	123_Y	1.028	0.67
208_V	218_A	1.026	0.67
85_N	90_K	1.025	0.67
150_E	171_L	1.018	0.66
231_R	345_Y	1.016	0.66
199_A	288_D	1.012	0.66
72_V	203_A	1.012	0.66
179_G	275_G	0.999	0.65
258_V	296_I	0.992	0.64
322_L	347_H	0.991	0.64
307_A	325_R	0.989	0.64
261_L	286_V	0.987	0.64
217_S	339_V	0.985	0.63
65_P	72_V	0.984	0.63
117_V	123_Y	0.982	0.63
216_V	303_D	0.978	0.63
74_A	271_D	0.977	0.63
223_Q	287_N	0.976	0.63
165_H	197_E	0.976	0.63
116_T	203_A	0.973	0.63
296_I	310_I	0.972	0.62
258_V	275_G	0.970	0.62
116_T	123_Y	0.965	0.62
198_S	214_G	0.960	0.61
256_G	370_E	0.958	0.61
216_V	318_T	0.958	0.61
164_I	200_P	0.957	0.61
113_G	116_T	0.954	0.61
208_V	226_M	0.954	0.61
73_Y	258_V	0.954	0.61
69_D	89_G	0.948	0.60
197_E	200_P	0.936	0.59
271_D	274_S	0.935	0.59
81_V	95_V	0.934	0.59
322_L	381_Q	0.934	0.59
349_I	356_F	0.932	0.59
332_L	337_L	0.931	0.59
233_S	262_A	0.929	0.59
249_T	258_V	0.928	0.59
179_G	224_G	0.920	0.58
203_A	296_I	0.918	0.58
284_G	304_R	0.913	0.58
208_V	283_L	0.911	0.57
359_Q	379_L	0.904	0.57
377_K	381_Q	0.904	0.57
358_A	370_E	0.896	0.56
209_V	267_L	0.893	0.56
205_G	220_L	0.892	0.56
223_Q	375_D	0.889	0.56
91_E	350_N	0.888	0.55
250_T	351_V	0.886	0.55
122_V	148_A	0.878	0.55
341_D	349_I	0.873	0.54
165_H	169_G	0.869	0.54
284_G	308_L	0.869	0.54
246_D	260_A	0.869	0.54
293_G	375_D	0.865	0.53
98_A	131_V	0.860	0.53
337_L	351_V	0.859	0.53
289_F	330_P	0.855	0.53
248_D	261_L	0.854	0.53
208_V	272_L	0.851	0.52
128_K	213_N	0.844	0.52
83_A	95_V	0.838	0.51
171_L	307_A	0.834	0.51
198_S	201_T	0.834	0.51
132_Y	178_D	0.831	0.51
122_V	207_A	0.829	0.50
117_V	280_K	0.828	0.50
257_V	271_D	0.823	0.50
359_Q	362_V	0.822	0.50
299_V	307_A	0.820	0.50
225_Q	351_V	0.816	0.49
125_G	158_S	0.816	0.49
116_T	264_N	0.814	0.49
297_Y	310_I	0.814	0.49
323_L	345_Y	0.813	0.49
251_P	332_L	0.813	0.49
84_L	91_E	0.811	0.49
253_V	259_F	0.810	0.49
77_R	165_H	0.810	0.49
172_Q	181_V	0.806	0.48
286_V	308_L	0.803	0.48
97_L	216_V	0.802	0.48
129_A	136_T	0.801	0.48
268_T	302_N	0.801	0.48
115_V	118_S	0.794	0.47
259_F	314_V	0.791	0.47
305_V	330_P	0.791	0.47
319_Q	337_L	0.789	0.47
320_S	337_L	0.789	0.47
209_V	213_N	0.788	0.47
350_N	380_I	0.787	0.47
274_S	352_E	0.782	0.46
64_H	67_L	0.781	0.46
81_V	225_Q	0.778	0.46
275_G	312_G	0.777	0.46
306_M	315_T	0.775	0.46
308_L	313_G	0.774	0.46
299_V	330_P	0.772	0.45
85_N	142_A	0.766	0.45
262_A	306_M	0.761	0.45
300_D	305_V	0.759	0.44
342_S	350_N	0.758	0.44
94_S	326_L	0.757	0.44
206_A	218_A	0.756	0.44
254_V	290_I	0.753	0.44
356_F	372_V	0.753	0.44
231_R	296_I	0.751	0.44
94_S	288_D	0.749	0.43
365_S	372_V	0.748	0.43
253_V	325_R	0.748	0.43
113_G	117_V	0.745	0.43
94_S	124_I	0.741	0.43
262_A	270_L	0.740	0.43
88_D	99_E	0.740	0.43
175_N	264_N	0.739	0.43
270_L	349_I	0.736	0.42
276_Q	336_N	0.736	0.42
334_N	338_V	0.735	0.42
114_G	117_V	0.734	0.42
163_L	166_T	0.734	0.42
289_F	296_I	0.734	0.42
79_G	337_L	0.733	0.42
313_G	372_V	0.731	0.42
348_W	360_Q	0.731	0.42
225_Q	276_Q	0.727	0.42
340_G	367_F	0.726	0.42
216_V	260_A	0.723	0.41
72_V	159_D	0.723	0.41
132_Y	139_G	0.716	0.41
81_V	173_A	0.713	0.40
205_G	208_V	0.707	0.40
312_G	366_G	0.704	0.40
256_G	294_N	0.703	0.40
259_F	267_L	0.702	0.40
333_Y	339_V	0.701	0.39
147_V	174_L	0.699	0.39
250_T	259_F	0.697	0.39
99_E	197_E	0.697	0.39
66_A	331_V	0.696	0.39
271_D	359_Q	0.695	0.39
67_L	70_N	0.694	0.39
86_A	122_V	0.694	0.39
327_L	349_I	0.693	0.39
216_V	304_R	0.693	0.39
363_D	372_V	0.692	0.39
260_A	264_N	0.692	0.39
125_G	152_L	0.692	0.39
87_D	131_V	0.691	0.39
159_D	164_I	0.689	0.38
162_V	281_R	0.688	0.38
344_G	362_V	0.687	0.38
378_L	381_Q	0.686	0.38
152_L	203_A	0.686	0.38
139_G	255_N	0.686	0.38
111_L	209_V	0.683	0.38
72_V	127_E	0.679	0.38
162_V	207_A	0.674	0.37
188_D	209_V	0.672	0.37
216_V	281_R	0.671	0.37
156_V	201_T	0.670	0.37
162_V	330_P	0.670	0.37
155_P	331_V	0.670	0.37
354_G	375_D	0.669	0.37
198_S	216_V	0.665	0.37
131_V	316_L	0.664	0.36
224_G	275_G	0.663	0.36
328_T	346_L	0.662	0.36
353_D	374_A	0.661	0.36
133_A	142_A	0.661	0.36
262_A	268_T	0.659	0.36
64_H	122_V	0.658	0.36
368_Q	375_D	0.658	0.36
252_V	367_F	0.657	0.36
233_S	246_D	0.657	0.36
292_D	295_R	0.657	0.36
217_S	229_Q	0.656	0.36
131_V	322_L	0.655	0.36
64_H	343_E	0.653	0.36
378_L	382_A	0.650	0.35
346_L	362_V	0.646	0.35
270_L	308_L	0.645	0.35
166_T	204_F	0.643	0.35
62_N	68_A	0.642	0.35
268_T	277_I	0.641	0.35
122_V	157_V	0.641	0.35
157_V	163_L	0.640	0.35
253_V	293_G	0.639	0.35
295_R	341_D	0.636	0.34
233_S	284_G	0.636	0.34
75_A	79_G	0.636	0.34
220_L	356_F	0.635	0.34
357_V	364_S	0.634	0.34
129_A	145_T	0.632	0.34
73_Y	83_A	0.631	0.34
228_W	338_V	0.630	0.34
164_I	174_L	0.629	0.34
65_P	86_A	0.627	0.34
217_S	332_L	0.626	0.33
224_G	346_L	0.624	0.33
132_Y	176_E	0.623	0.33
356_F	375_D	0.623	0.33
217_S	285_S	0.621	0.33
198_S	330_P	0.615	0.33
129_A	289_F	0.611	0.32
307_A	351_V	0.611	0.32
232_I	252_V	0.610	0.32
113_G	278_M	0.609	0.32
196_G	206_A	0.607	0.32
214_G	248_D	0.606	0.32
276_Q	372_V	0.605	0.32
299_V	339_V	0.604	0.32
346_L	370_E	0.603	0.32
281_R	292_D	0.601	0.32
166_T	295_R	0.601	0.32
190_P	305_V	0.600	0.32
246_D	262_A	0.598	0.31
358_A	362_V	0.595	0.31
116_T	153_S	0.594	0.31
116_T	133_A	0.593	0.31
116_T	150_E	0.592	0.31
290_I	294_N	0.592	0.31
81_V	337_L	0.590	0.31
128_K	370_E	0.590	0.31
121_H	161_L	0.590	0.31
76_D	83_A	0.587	0.31
167_S	302_N	0.587	0.31
112_S	117_V	0.584	0.30
337_L	355_R	0.584	0.30
115_V	201_T	0.583	0.30
257_V	339_V	0.583	0.30
220_L	361_K	0.582	0.30
292_D	381_Q	0.582	0.30
286_V	312_G	0.580	0.30
265_G	344_G	0.579	0.30
356_F	363_D	0.576	0.30
159_D	338_V	0.576	0.30
346_L	367_F	0.574	0.30
373_A	377_K	0.573	0.30
226_M	340_G	0.573	0.30
374_A	380_I	0.573	0.30
337_L	344_G	0.571	0.29
366_G	382_A	0.571	0.29
368_Q	371_P	0.570	0.29
203_A	254_V	0.569	0.29
368_Q	381_Q	0.568	0.29
231_R	337_L	0.565	0.29
293_G	332_L	0.563	0.29
196_G	268_T	0.563	0.29
264_N	270_L	0.562	0.29
134_L	278_M	0.562	0.29
132_Y	325_R	0.561	0.29
188_D	211_G	0.560	0.29
257_V	336_N	0.560	0.29
81_V	133_A	0.558	0.28
88_D	131_V	0.558	0.28
335_G	339_V	0.557	0.28
228_W	233_S	0.556	0.28
198_S	203_A	0.556	0.28
64_H	165_H	0.555	0.28
279_W	289_F	0.554	0.28
208_V	347_H	0.554	0.28
346_L	357_V	0.553	0.28
98_A	158_S	0.551	0.28
265_G	380_I	0.551	0.28
198_S	225_Q	0.551	0.28
132_Y	161_L	0.548	0.28
169_G	356_F	0.548	0.28
92_I	114_G	0.547	0.28
88_D	139_G	0.547	0.28
362_V	377_K	0.547	0.28
125_G	229_Q	0.547	0.28
213_N	330_P	0.546	0.28
81_V	171_L	0.546	0.28
208_V	255_N	0.545	0.28
133_A	260_A	0.543	0.27
108_P	379_L	0.543	0.27
150_E	258_V	0.542	0.27
216_V	245_S	0.542	0.27
354_G	357_V	0.540	0.27
284_G	306_M	0.540	0.27
178_D	305_V	0.539	0.27
116_T	217_S	0.537	0.27
66_A	115_V	0.537	0.27
309_T	317_W	0.534	0.27
204_F	212_D	0.533	0.27
133_A	173_A	0.533	0.27
112_S	220_L	0.532	0.27
249_T	291_V	0.531	0.27
203_A	282_E	0.530	0.27
274_S	299_V	0.529	0.26
132_Y	141_V	0.528	0.26
170_Q	176_E	0.526	0.26
113_G	122_V	0.525	0.26
148_A	214_G	0.524	0.26
250_T	270_L	0.524	0.26
204_F	372_V	0.523	0.26
155_P	234_Q	0.523	0.26
210_G	233_S	0.522	0.26
158_S	359_Q	0.522	0.26
112_S	260_A	0.521	0.26
371_P	375_D	0.519	0.26
160_G	297_Y	0.518	0.26
181_V	184_T	0.516	0.26
78_A	83_A	0.516	0.26
168_N	210_G	0.514	0.25
302_N	341_D	0.514	0.25
216_V	222_E	0.513	0.25
202_T	269_A	0.513	0.25
213_N	276_Q	0.510	0.25
310_I	335_G	0.510	0.25
200_P	276_Q	0.508	0.25
360_Q	367_F	0.507	0.25
71_V	288_D	0.507	0.25
285_S	307_A	0.507	0.25
299_V	323_L	0.506	0.25
211_G	214_G	0.506	0.25
136_T	275_G	0.505	0.25
274_S	291_V	0.504	0.25
135_N	201_T	0.503	0.25
228_W	253_V	0.503	0.25
116_T	157_V	0.503	0.25
347_H	363_D	0.502	0.25
289_F	328_T	0.501	0.25
230_Q	270_L	0.501	0.25
361_K	378_L	0.501	0.25
325_R	340_G	0.500	0.25
93_W	201_T	0.500	0.25
251_P	372_V	0.500	0.25
218_A	262_A	0.500	0.25

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
2ovrB	1	0.8801	100	0.393	Contact Map
4wjuA	1	0.9056	100	0.399	Contact Map
1vyhC	1	0.7296	100	0.401	Contact Map
4nsxA	1	0.9439	100	0.404	Contact Map
4j87A	1	0.7168	100	0.412	Contact Map
4wjsA	1	0.9362	100	0.415	Contact Map
4bzjA	2	0.7985	100	0.42	Contact Map
3sfzA	1	0.9337	100	0.422	Contact Map
4j73A	1	0.7092	100	0.423	Contact Map
2pm9A	1	0.801	100	0.428	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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