RPOH - ECOLI - GREMLIN Contacts

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RPOH - RNA polymerase sigma factor RpoH

UniProt:	P0AGB3	Sequences: MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10897
Length:	284 (237)
Sequences:	7240 (4282)
Seq/√Len:	278.1

ECOLI - RPOH RPOD RPOS FLIA
BACSU - SIGA RPSK RPSG RPSF RPSB RPSD RPSE RPSH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_T	146_L	3.695	1.00
50_A	91_R	3.557	1.00
145_R	160_E	3.552	1.00
148_W	156_M	3.373	1.00
61_V	82_G	3.119	1.00
155_E	165_S	3.093	1.00
237_Q	241_R	3.029	1.00
262_V	267_V	2.909	1.00
141_K	160_E	2.879	1.00
40_K	46_D	2.868	1.00
51_K	55_L	2.773	1.00
138_N	160_E	2.423	1.00
33_E	52_T	2.404	1.00
36_A	40_K	2.367	1.00
242_A	259_R	2.241	1.00
236_S	277_K	2.198	1.00
266_R	269_Q	2.192	1.00
154_V	169_R	2.115	1.00
238_D	259_R	2.080	1.00
60_F	102_V	2.079	1.00
242_A	251_S	2.064	1.00
243_R	271_E	2.019	1.00
164_T	167_D	2.015	1.00
231_G	281_A	2.006	1.00
254_Q	258_D	1.990	1.00
230_Q	237_Q	1.961	1.00
251_S	259_R	1.955	1.00
94_N	97_V	1.919	1.00
241_R	246_D	1.907	1.00
58_L	83_N	1.851	1.00
238_D	242_A	1.848	1.00
238_D	260_Y	1.812	1.00
64_I	106_V	1.803	1.00
260_Y	267_V	1.752	1.00
239_I	270_L	1.750	1.00
92_R	104_F	1.738	1.00
155_E	159_R	1.731	1.00
233_D	277_K	1.711	1.00
81_E	116_Y	1.706	1.00
142_T	152_D	1.693	1.00
141_K	145_R	1.687	1.00
265_E	268_R	1.667	1.00
157_V	168_V	1.660	1.00
52_T	56_S	1.640	1.00
239_I	274_A	1.627	1.00
64_I	113_I	1.621	1.00
135_L	171_M	1.619	1.00
154_V	165_S	1.613	1.00
154_V	172_E	1.591	1.00
100_R	103_S	1.552	1.00
62_V	79_I	1.551	1.00
54_I	87_M	1.548	1.00
135_L	157_V	1.527	1.00
138_N	141_K	1.526	1.00
47_L	51_K	1.491	1.00
65_A	79_I	1.489	1.00
154_V	168_V	1.463	1.00
35_R	39_E	1.462	1.00
42_H	96_E	1.448	1.00
251_S	255_E	1.445	1.00
79_I	83_N	1.430	1.00
65_A	113_I	1.403	1.00
165_S	169_R	1.401	1.00
82_G	113_I	1.356	1.00
142_T	148_W	1.350	1.00
233_D	236_S	1.349	1.00
138_N	142_T	1.338	1.00
266_R	270_L	1.316	1.00
163_V	171_M	1.305	1.00
139_L	172_E	1.305	1.00
135_L	161_L	1.302	1.00
236_S	273_N	1.298	1.00
101_L	105_A	1.273	1.00
138_N	161_L	1.273	1.00
142_T	160_E	1.255	1.00
253_L	257_A	1.248	1.00
183_D	196_A	1.247	1.00
158_A	165_S	1.245	1.00
220_Q	224_R	1.245	1.00
65_A	75_Q	1.243	1.00
240_I	278_L	1.235	1.00
90_V	101_L	1.233	1.00
42_H	95_P	1.210	1.00
163_V	168_V	1.208	1.00
152_D	156_M	1.206	1.00
39_E	96_E	1.199	1.00
158_A	168_V	1.196	1.00
153_E	156_M	1.187	1.00
202_Q	205_S	1.184	1.00
174_R	177_A	1.181	1.00
238_D	241_R	1.153	1.00
54_I	90_V	1.137	1.00
38_A	42_H	1.134	1.00
48_E	51_K	1.126	1.00
89_A	105_A	1.119	1.00
38_A	41_L	1.116	1.00
66_R	75_Q	1.103	1.00
33_E	36_A	1.102	1.00
73_L	116_Y	1.069	1.00
213_E	217_W	1.061	1.00
135_L	168_V	1.058	1.00
242_A	256_L	1.058	1.00
183_D	193_Q	1.057	1.00
270_L	274_A	1.054	1.00
219_E	223_N	1.053	1.00
218_E	222_A	1.052	1.00
48_E	52_T	1.046	1.00
265_E	269_Q	1.044	1.00
222_A	226_T	1.044	1.00
234_E	237_Q	1.042	1.00
137_F	141_K	1.037	1.00
192_S	200_Y	1.037	1.00
61_V	86_L	1.030	1.00
36_A	39_E	1.020	1.00
148_W	152_D	1.016	1.00
40_K	52_T	1.012	1.00
253_L	265_E	1.011	1.00
244_W	271_E	1.000	1.00
41_L	45_G	0.997	1.00
40_K	44_H	0.988	1.00
83_N	87_M	0.986	1.00
52_T	55_L	0.986	1.00
146_L	152_D	0.982	1.00
57_H	102_V	0.978	1.00
124_V	127_A	0.971	1.00
276_K	280_A	0.970	1.00
40_K	49_A	0.966	1.00
142_T	157_V	0.958	1.00
139_L	157_V	0.958	1.00
34_E	38_A	0.957	1.00
85_G	89_A	0.945	1.00
143_K	152_D	0.943	1.00
46_D	49_A	0.938	1.00
208_F	213_E	0.937	1.00
62_V	83_N	0.936	1.00
158_A	163_V	0.936	1.00
254_Q	257_A	0.933	1.00
39_E	95_P	0.928	1.00
235_R	270_L	0.926	1.00
254_Q	264_A	0.923	1.00
69_A	75_Q	0.908	1.00
239_I	260_Y	0.907	1.00
143_K	146_L	0.905	1.00
121_W	128_T	0.899	1.00
227_D	230_Q	0.897	1.00
66_R	69_A	0.897	1.00
253_L	268_R	0.891	1.00
110_K	114_H	0.889	1.00
235_R	266_R	0.886	1.00
75_Q	79_I	0.880	1.00
86_L	105_A	0.880	1.00
216_N	220_Q	0.879	1.00
235_R	239_I	0.876	1.00
64_I	110_K	0.873	1.00
146_L	156_M	0.868	1.00
224_R	227_D	0.866	1.00
239_I	262_V	0.864	1.00
37_L	52_T	0.864	1.00
53_L	90_V	0.856	1.00
243_R	256_L	0.854	1.00
68_Y	113_I	0.854	1.00
50_A	90_V	0.847	1.00
41_L	53_L	0.846	1.00
228_A	278_L	0.845	1.00
253_L	264_A	0.844	1.00
79_I	82_G	0.844	1.00
138_N	157_V	0.840	1.00
39_E	44_H	0.830	1.00
37_L	49_A	0.830	1.00
45_G	49_A	0.827	1.00
58_L	61_V	0.827	1.00
88_K	92_R	0.827	1.00
217_W	220_Q	0.825	1.00
92_R	108_W	0.824	1.00
223_N	227_D	0.824	1.00
135_L	172_E	0.822	0.99
168_V	172_E	0.814	0.99
108_W	111_A	0.813	0.99
62_V	75_Q	0.808	0.99
63_H	66_R	0.807	0.99
167_D	170_E	0.807	0.99
35_R	98_G	0.805	0.99
234_E	238_D	0.799	0.99
203_D	206_S	0.799	0.99
236_S	270_L	0.795	0.99
146_L	160_E	0.784	0.99
32_D	36_A	0.779	0.99
263_S	266_R	0.775	0.99
179_D	183_D	0.772	0.99
104_F	108_W	0.767	0.99
41_L	44_H	0.761	0.99
111_A	118_L	0.761	0.99
180_M	184_L	0.759	0.99
118_L	128_T	0.756	0.99
61_V	83_N	0.755	0.99
229_M	241_R	0.753	0.99
133_R	136_F	0.749	0.99
89_A	101_L	0.748	0.99
226_T	241_R	0.747	0.99
60_F	103_S	0.745	0.99
53_L	57_H	0.742	0.99
130_K	171_M	0.738	0.99
105_A	109_I	0.738	0.99
181_T	185_S	0.735	0.99
37_L	41_L	0.731	0.99
242_A	246_D	0.731	0.99
213_E	216_N	0.730	0.99
142_T	156_M	0.728	0.99
42_H	45_G	0.727	0.99
241_R	245_L	0.725	0.99
108_W	268_R	0.725	0.99
220_Q	223_N	0.724	0.99
253_L	266_R	0.715	0.99
138_N	146_L	0.711	0.99
60_F	106_V	0.711	0.99
117_V	128_T	0.706	0.98
178_Q	183_D	0.705	0.98
39_E	42_H	0.703	0.98
88_K	112_E	0.701	0.98
233_D	274_A	0.699	0.98
33_E	37_L	0.691	0.98
263_S	269_Q	0.688	0.98
108_W	265_E	0.688	0.98
148_W	153_E	0.687	0.98
95_P	98_G	0.686	0.98
253_L	269_Q	0.686	0.98
42_H	94_N	0.683	0.98
136_F	139_L	0.680	0.98
139_L	143_K	0.679	0.98
196_A	200_Y	0.679	0.98
271_E	274_A	0.676	0.98
256_L	271_E	0.676	0.98
63_H	67_N	0.674	0.98
255_E	258_D	0.667	0.98
56_S	59_R	0.665	0.98
143_K	151_Q	0.663	0.98
111_A	115_E	0.663	0.98
115_E	119_R	0.661	0.98
158_A	161_L	0.657	0.98
84_I	87_M	0.657	0.98
181_T	184_L	0.657	0.98
116_Y	120_N	0.652	0.97
243_R	253_L	0.648	0.97
61_V	113_I	0.648	0.97
104_F	107_H	0.646	0.97
99_V	103_S	0.645	0.97
88_K	104_F	0.643	0.97
103_S	106_V	0.642	0.97
59_R	62_V	0.640	0.97
159_R	162_G	0.638	0.97
153_E	157_V	0.637	0.97
62_V	76_A	0.634	0.97
111_A	128_T	0.633	0.97
87_M	90_V	0.632	0.97
240_I	275_M	0.628	0.97
243_R	252_T	0.626	0.97
236_S	274_A	0.625	0.97
219_E	222_A	0.624	0.97
212_I	216_N	0.624	0.97
139_L	151_Q	0.623	0.97
111_A	268_R	0.619	0.96
262_V	266_R	0.613	0.96
179_D	182_F	0.613	0.96
38_A	95_P	0.613	0.96
228_A	281_A	0.610	0.96
168_V	171_M	0.609	0.96
115_E	243_R	0.609	0.96
244_W	275_M	0.606	0.96
58_L	62_V	0.605	0.96
257_A	264_A	0.604	0.96
235_R	262_V	0.603	0.96
114_H	128_T	0.602	0.96
85_G	113_I	0.602	0.96
180_M	183_D	0.601	0.96
257_A	265_E	0.600	0.96
73_L	78_L	0.600	0.96
158_A	164_T	0.599	0.96
152_D	157_V	0.599	0.96
253_L	271_E	0.595	0.96
78_L	116_Y	0.593	0.96
40_K	45_G	0.592	0.95
229_M	233_D	0.590	0.95
161_L	168_V	0.590	0.95
112_E	116_Y	0.589	0.95
221_A	228_A	0.588	0.95
41_L	90_V	0.587	0.95
215_D	219_E	0.586	0.95
126_V	130_K	0.586	0.95
88_K	91_R	0.583	0.95
195_M	205_S	0.582	0.95
214_D	217_W	0.582	0.95
156_M	160_E	0.574	0.95
243_R	264_A	0.573	0.95
35_R	42_H	0.572	0.95
235_R	269_Q	0.569	0.94
142_T	145_R	0.569	0.94
62_V	65_A	0.566	0.94
147_G	152_D	0.563	0.94
38_A	90_V	0.563	0.94
204_K	207_N	0.562	0.94
202_Q	206_S	0.561	0.94
34_E	56_S	0.561	0.94
137_F	140_R	0.560	0.94
134_K	137_F	0.559	0.94
246_D	251_S	0.557	0.94
58_L	79_I	0.553	0.94
228_A	274_A	0.553	0.94
256_L	260_Y	0.550	0.93
115_E	127_A	0.550	0.93
192_S	197_P	0.547	0.93
216_N	219_E	0.547	0.93
129_T	134_K	0.547	0.93
171_M	174_R	0.546	0.93
233_D	270_L	0.544	0.93
127_A	268_R	0.544	0.93
119_R	128_T	0.542	0.93
90_V	95_P	0.540	0.93
128_T	268_R	0.540	0.93
80_Q	84_I	0.540	0.93
44_H	49_A	0.540	0.93
185_S	191_D	0.537	0.93
115_E	124_V	0.536	0.92
122_R	126_V	0.533	0.92
93_F	99_V	0.531	0.92
187_D	190_S	0.529	0.92
225_L	228_A	0.529	0.92
229_M	237_Q	0.528	0.92
57_H	61_V	0.528	0.92
226_T	230_Q	0.526	0.92
197_P	202_Q	0.521	0.91
257_A	268_R	0.518	0.91
185_S	193_Q	0.518	0.91
47_L	50_A	0.518	0.91
122_R	131_A	0.517	0.91
51_K	78_L	0.517	0.91
264_A	269_Q	0.517	0.91
180_M	185_S	0.516	0.91
200_Y	205_S	0.516	0.91
64_I	109_I	0.516	0.91
154_V	161_L	0.514	0.91
34_E	100_R	0.513	0.91
133_R	137_F	0.512	0.91
65_A	74_P	0.512	0.91
135_L	138_N	0.509	0.90
191_D	197_P	0.508	0.90
106_V	263_S	0.507	0.90
186_S	200_Y	0.507	0.90
118_L	132_Q	0.506	0.90
136_F	259_R	0.506	0.90
179_D	185_S	0.506	0.90
197_P	201_L	0.505	0.90
258_D	261_G	0.503	0.90
41_L	46_D	0.503	0.90
85_G	109_I	0.503	0.90
115_E	252_T	0.502	0.90
129_T	132_Q	0.500	0.90

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
1l9zH	1	0.8908	100	0.243	Contact Map
2a6hF	1	0.919	100	0.244	Contact Map
4yfkF	1	0.9648	100	0.347	Contact Map
1l0oC	1	0.1937	100	0.49	Contact Map
1rp3A	1	0.8028	100	0.524	Contact Map
3ugoA	1	0.3908	100	0.546	Contact Map
4nqwA	1	0.5211	99.9	0.646	Contact Map
1or7A	2	0.6373	99.9	0.682	Contact Map
4cxfA	1	0.5352	99.8	0.688	Contact Map
2q1zA	1	0.6162	99.8	0.696	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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