BAMD - ECOLI - GREMLIN Contacts

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BAMD - Outer membrane protein assembly factor BamD

UniProt:	P0AC02	Sequences: MTRMKYLVAAATLSLFLAGCSGSKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14222
Length:	245 (186)
Sequences:	14078 (12518)
Seq/√Len:	917.9

ECOLI - BAMD LPSRP NLPI HEMY YFBP NRFG PGAA YGEH BCSC
BACSU - YVCD YPIA RAPK RAPF RAPC RAPD RAPH RAPG RAPB RAPJ RAPE RAPI RAPA YRRB YSOA
HALSA - Q9HMM8
SULSO - Q97V36 Q97WM3 Q97VC4 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_D	87_L	3.596	1.00
227_M	230_Q	3.586	1.00
139_H	142_A	3.389	1.00
47_N	50_Q	3.291	1.00
190_A	193_A	2.992	1.00
76_I	92_I	2.894	1.00
35_I	54_Q	2.756	1.00
39_A	55_L	2.753	1.00
219_E	235_A	2.575	1.00
55_L	74_D	2.448	1.00
72_Q	91_A	2.411	1.00
56_E	75_L	2.303	1.00
38_T	54_Q	2.212	1.00
79_Y	91_A	2.207	1.00
215_L	234_V	2.159	1.00
42_K	50_Q	2.114	1.00
75_L	91_A	2.091	1.00
198_V	217_L	2.057	1.00
178_E	197_R	2.029	1.00
93_D	112_R	2.023	1.00
199_E	218_M	1.969	1.00
182_A	198_V	1.967	1.00
42_K	54_Q	1.915	1.00
79_Y	87_L	1.903	1.00
92_I	111_M	1.844	1.00
89_Q	93_D	1.736	1.00
79_Y	84_D	1.666	1.00
195_V	222_Y	1.649	1.00
218_M	222_Y	1.643	1.00
52_I	79_Y	1.582	1.00
195_V	199_E	1.564	1.00
52_I	56_E	1.532	1.00
195_V	225_M	1.491	1.00
38_T	42_K	1.488	1.00
112_R	116_N	1.486	1.00
232_E	236_K	1.486	1.00
35_I	57_A	1.461	1.00
42_K	47_N	1.460	1.00
144_F	148_S	1.458	1.00
222_Y	230_Q	1.454	1.00
218_M	234_V	1.434	1.00
181_V	197_R	1.417	1.00
201_M	214_A	1.353	1.00
222_Y	234_V	1.350	1.00
195_V	218_M	1.343	1.00
95_F	108_V	1.337	1.00
215_L	237_I	1.335	1.00
75_L	79_Y	1.334	1.00
185_Y	193_A	1.332	1.00
58_L	71_V	1.331	1.00
185_Y	197_R	1.329	1.00
89_Q	116_N	1.327	1.00
96_I	109_M	1.308	1.00
52_I	82_N	1.306	1.00
32_P	58_L	1.305	1.00
41_Q	45_D	1.304	1.00
183_E	217_L	1.299	1.00
59_D	71_V	1.287	1.00
36_Y	40_Q	1.213	1.00
222_Y	227_M	1.195	1.00
73_L	77_Y	1.190	1.00
219_E	231_A	1.187	1.00
52_I	78_A	1.180	1.00
89_Q	112_R	1.175	1.00
40_Q	74_D	1.174	1.00
52_I	75_L	1.161	1.00
186_T	217_L	1.147	1.00
230_Q	233_K	1.139	1.00
50_Q	53_T	1.124	1.00
147_F	163_A	1.124	1.00
142_A	145_S	1.119	1.00
74_D	77_Y	1.115	1.00
202_L	215_L	1.098	1.00
146_D	149_K	1.089	1.00
219_E	238_I	1.089	1.00
54_Q	57_A	1.085	1.00
76_I	95_F	1.084	1.00
181_V	185_Y	1.081	1.00
164_T	168_V	1.077	1.00
195_V	221_A	1.065	1.00
49_R	82_N	1.061	1.00
223_R	231_A	1.057	1.00
178_E	200_G	1.054	1.00
72_Q	94_R	1.054	1.00
110_Y	114_L	1.048	1.00
59_D	72_Q	1.048	1.00
39_A	58_L	1.045	1.00
215_L	238_I	1.015	1.00
221_A	225_M	1.008	1.00
217_L	220_N	1.004	1.00
182_A	194_V	1.004	1.00
36_Y	74_D	0.996	1.00
69_Q	95_F	0.994	1.00
192_V	225_M	0.993	1.00
186_T	221_A	0.989	1.00
109_M	146_D	0.985	1.00
78_A	82_N	0.984	1.00
150_L	160_T	0.978	1.00
80_Y	111_M	0.966	1.00
193_A	197_R	0.959	1.00
205_Y	208_T	0.954	1.00
72_Q	95_F	0.950	1.00
87_L	90_A	0.949	1.00
179_Y	217_L	0.947	1.00
182_A	201_M	0.937	1.00
91_A	94_R	0.935	1.00
76_I	88_A	0.929	1.00
35_I	58_L	0.924	1.00
202_L	218_M	0.923	1.00
223_R	228_N	0.923	1.00
216_P	220_N	0.918	1.00
197_R	200_G	0.916	1.00
48_W	78_A	0.910	1.00
94_R	98_L	0.906	1.00
43_L	78_A	0.900	1.00
77_Y	111_M	0.898	1.00
113_G	147_F	0.891	1.00
157_S	160_T	0.890	1.00
202_L	214_A	0.888	1.00
43_L	74_D	0.887	1.00
116_N	146_D	0.886	1.00
148_S	164_T	0.871	1.00
180_S	183_E	0.867	1.00
112_R	146_D	0.865	1.00
73_L	108_V	0.864	1.00
96_I	108_V	0.864	1.00
99_N	102_H	0.862	1.00
142_A	146_D	0.862	1.00
199_E	230_Q	0.857	1.00
185_Y	190_A	0.853	1.00
36_Y	71_V	0.850	1.00
77_Y	92_I	0.849	1.00
40_Q	55_L	0.845	1.00
150_L	153_G	0.837	1.00
183_E	186_T	0.836	1.00
165_K	169_F	0.833	1.00
80_Y	92_I	0.829	1.00
149_K	153_G	0.827	1.00
149_K	152_R	0.826	1.00
40_Q	44_Q	0.821	1.00
43_L	55_L	0.820	1.00
37_A	40_Q	0.818	1.00
111_M	114_L	0.809	1.00
51_A	55_L	0.809	1.00
162_D	165_K	0.804	1.00
114_L	118_A	0.798	1.00
40_Q	43_L	0.795	1.00
89_Q	115_T	0.792	1.00
80_Y	118_A	0.787	1.00
184_Y	188_R	0.785	1.00
179_Y	183_E	0.782	1.00
53_T	57_A	0.777	1.00
39_A	51_A	0.774	1.00
59_D	75_L	0.770	1.00
58_L	61_R	0.769	1.00
43_L	48_W	0.767	1.00
102_H	108_V	0.767	1.00
200_G	204_D	0.766	1.00
193_A	196_N	0.766	1.00
80_Y	115_T	0.758	1.00
35_I	61_R	0.757	1.00
191_W	221_A	0.755	1.00
36_Y	58_L	0.749	1.00
154_Y	157_S	0.748	1.00
223_R	235_A	0.747	1.00
165_K	168_V	0.746	1.00
191_W	225_M	0.737	1.00
28_P	31_P	0.732	1.00
48_W	82_N	0.732	1.00
148_S	152_R	0.730	1.00
92_I	115_T	0.729	1.00
57_A	60_N	0.725	1.00
110_Y	113_G	0.722	1.00
173_R	176_K	0.720	1.00
200_G	203_R	0.714	1.00
183_E	187_E	0.714	1.00
94_R	97_R	0.711	1.00
191_W	224_Q	0.711	1.00
146_D	150_L	0.710	1.00
186_T	224_Q	0.706	1.00
80_Y	85_L	0.700	1.00
195_V	227_M	0.700	1.00
73_L	111_M	0.699	1.00
150_L	154_Y	0.698	1.00
62_Y	65_G	0.695	1.00
234_V	237_I	0.694	1.00
56_E	87_L	0.693	1.00
174_L	177_Y	0.691	1.00
34_E	38_T	0.689	1.00
48_W	81_K	0.689	1.00
144_F	168_V	0.679	1.00
220_N	224_Q	0.679	1.00
228_N	232_E	0.677	1.00
194_V	221_A	0.677	1.00
80_Y	88_A	0.669	1.00
163_A	166_R	0.668	1.00
201_M	204_D	0.667	1.00
85_L	115_T	0.664	1.00
191_W	195_V	0.664	1.00
178_E	204_D	0.664	1.00
55_L	58_L	0.662	1.00
114_L	117_M	0.662	1.00
89_Q	137_P	0.659	1.00
168_V	173_R	0.652	1.00
54_Q	58_L	0.651	1.00
55_L	78_A	0.650	1.00
53_T	56_E	0.650	1.00
93_D	97_R	0.646	1.00
38_T	41_Q	0.643	1.00
77_Y	81_K	0.641	1.00
145_S	148_S	0.641	1.00
48_W	52_I	0.632	1.00
212_R	238_I	0.632	1.00
43_L	51_A	0.631	1.00
57_A	61_R	0.630	1.00
186_T	191_W	0.630	1.00
198_V	218_M	0.629	1.00
102_H	107_Y	0.628	1.00
55_L	75_L	0.628	1.00
70_Q	74_D	0.627	1.00
198_V	221_A	0.627	1.00
185_Y	188_R	0.626	1.00
212_R	216_P	0.625	1.00
87_L	91_A	0.625	1.00
236_K	239_A	0.621	1.00
79_Y	82_N	0.617	1.00
31_P	34_E	0.617	1.00
50_Q	54_Q	0.614	1.00
196_N	199_E	0.611	1.00
77_Y	80_Y	0.609	1.00
233_K	237_I	0.605	1.00
199_E	222_Y	0.604	1.00
73_L	95_F	0.598	1.00
236_K	240_A	0.598	1.00
72_Q	98_L	0.595	1.00
186_T	194_V	0.595	1.00
85_L	118_A	0.592	1.00
229_A	233_K	0.587	1.00
91_A	95_F	0.586	1.00
192_V	195_V	0.585	1.00
86_P	90_A	0.584	1.00
235_A	239_A	0.580	1.00
145_S	149_K	0.577	1.00
52_I	84_D	0.574	1.00
144_F	171_K	0.573	1.00
116_N	142_A	0.570	1.00
222_Y	225_M	0.568	1.00
182_A	186_T	0.566	1.00
168_V	171_K	0.565	1.00
56_E	59_D	0.560	1.00
201_M	208_T	0.560	1.00
85_L	89_Q	0.558	1.00
179_Y	182_A	0.558	1.00
162_D	166_R	0.550	1.00
192_V	196_N	0.541	1.00
178_E	201_M	0.539	1.00
143_A	147_F	0.534	1.00
212_R	219_E	0.529	1.00
35_I	38_T	0.529	1.00
88_A	92_I	0.527	1.00
165_K	172_D	0.527	1.00
34_E	41_Q	0.526	1.00
140_A	144_F	0.526	1.00
49_R	52_I	0.523	1.00
69_Q	99_N	0.521	1.00
96_I	112_R	0.517	1.00
43_L	81_K	0.516	1.00
234_V	238_I	0.515	1.00
147_F	151_V	0.514	1.00
219_E	234_V	0.512	1.00
141_R	145_S	0.511	1.00
92_I	112_R	0.509	1.00
32_P	65_G	0.507	1.00
216_P	238_I	0.505	1.00
229_A	232_E	0.504	1.00
237_I	240_A	0.503	1.00
168_V	172_D	0.503	1.00
148_S	151_V	0.502	1.00
231_A	235_A	0.500	1.00

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
3qkyA	1	0.849	99.9	0.31	Contact Map
1w3bA	2	0.9633	99.9	0.34	Contact Map
2yhcA	1	0.8204	99.9	0.345	Contact Map
3q7aA	1	0.9306	99.9	0.356	Contact Map
3dssA	1	0.9388	99.9	0.363	Contact Map
4ui9J	2	0.8898	99.9	0.363	Contact Map
1dceA	1	0.8776	99.9	0.368	Contact Map
4ui9C	2	0.8898	99.9	0.369	Contact Map
4gywA	2	0.7061	99.9	0.369	Contact Map
4l9pA	1	0.9347	99.9	0.37	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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