RPSK - BACSU - GREMLIN Contacts

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RPSK - RNA polymerase sigma-K factor

UniProt:	P12254	Sequences: MVTGVFAALGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEIVITKGGCIHPSLIRFNIYGVRIHNGNFFHDKVNNCFFIFKSMPPLFVMNNEILMHLRALKKTKKDVSLHDPIGQDKEGNEISLIDVLKSENEDVIDTIQLNMELEKVKQYIDILDDREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKMFHEFYRAEKEKRKKAKGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	294 (243)
Sequences:	6535 (3850)
Seq/√Len:	247.0

ECOLI - RPOD RPOS RPOH FLIA
BACSU - RPSK SIGA RPSB RPSG RPSF 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
147_V	151_F	3.690	1.00
52_R	93_E	3.600	1.00
153_I	159_P	3.489	1.00
234_K	238_V	3.465	1.00
43_L	48_D	3.350	1.00
63_V	84_G	3.234	1.00
260_I	265_V	3.006	1.00
158_P	168_L	2.934	1.00
53_N	57_E	2.924	1.00
146_K	163_M	2.765	1.00
150_C	163_M	2.765	1.00
36_E	54_M	2.754	1.00
39_K	43_L	2.463	1.00
264_Y	267_R	2.385	1.00
239_G	257_E	2.358	1.00
143_F	163_M	2.312	1.00
233_E	275_K	2.257	1.00
240_R	269_E	2.223	1.00
62_L	104_A	2.211	1.00
235_E	257_E	2.176	1.00
239_G	249_K	2.140	1.00
228_I	279_E	2.124	1.00
184_H	197_S	1.992	1.00
235_E	258_L	1.957	1.00
167_I	170_H	1.957	1.00
249_K	257_E	1.940	1.00
157_M	172_R	1.940	1.00
227_D	234_K	1.915	1.00
263_S	266_S	1.909	1.00
258_L	265_V	1.864	1.00
96_S	99_K	1.857	1.00
252_R	256_K	1.855	1.00
60_L	85_T	1.811	1.00
230_D	275_K	1.808	1.00
235_E	239_G	1.807	1.00
236_V	268_I	1.787	1.00
66_I	108_A	1.780	1.00
42_E	46_K	1.764	1.00
147_V	153_I	1.762	1.00
146_K	150_C	1.724	1.00
56_I	89_I	1.720	1.00
147_V	155_K	1.708	1.00
210_I	214_Q	1.693	1.00
236_V	272_A	1.677	1.00
160_L	171_L	1.642	1.00
94_S	106_Y	1.635	1.00
33_S	36_E	1.618	1.00
143_F	147_V	1.599	1.00
67_V	81_I	1.561	1.00
54_M	58_H	1.557	1.00
184_H	199_I	1.555	1.00
66_I	115_I	1.552	1.00
49_E	53_N	1.550	1.00
45_A	98_G	1.540	1.00
158_P	162_V	1.534	1.00
83_I	120_G	1.526	1.00
38_K	42_E	1.517	1.00
34_S	38_K	1.499	1.00
230_D	233_E	1.482	1.00
157_M	171_L	1.479	1.00
64_A	81_I	1.474	1.00
102_K	105_T	1.473	1.00
157_M	168_L	1.448	1.00
161_F	171_L	1.431	1.00
81_I	85_T	1.426	1.00
168_L	172_R	1.396	1.00
45_A	97_A	1.383	1.00
249_K	253_E	1.379	1.00
166_E	171_L	1.370	1.00
67_V	115_I	1.338	1.00
237_I	276_M	1.316	1.00
155_K	159_P	1.311	1.00
143_F	146_K	1.292	1.00
42_E	98_G	1.287	1.00
233_E	271_R	1.267	1.00
91_G	107_A	1.252	1.00
143_F	164_N	1.247	1.00
217_M	221_K	1.244	1.00
50_H	53_N	1.226	1.00
41_L	44_M	1.216	1.00
56_I	92_I	1.208	1.00
48_D	51_A	1.207	1.00
147_V	163_M	1.202	1.00
84_G	115_I	1.194	1.00
67_V	77_A	1.187	1.00
208_D	211_D	1.176	1.00
43_L	54_M	1.159	1.00
161_F	166_E	1.156	1.00
193_G	201_V	1.155	1.00
136_R	140_G	1.148	1.00
92_I	103_L	1.145	1.00
36_E	39_K	1.145	1.00
264_Y	268_I	1.138	1.00
263_S	267_R	1.125	1.00
103_L	107_A	1.125	1.00
156_S	159_P	1.122	1.00
251_Q	255_A	1.111	1.00
231_D	234_K	1.107	1.00
137_I	170_H	1.094	1.00
251_Q	263_S	1.092	1.00
50_H	54_M	1.087	1.00
278_H	281_Y	1.081	1.00
41_L	45_A	1.080	1.00
119_K	123_I	1.078	1.00
268_I	272_A	1.075	1.00
235_E	238_V	1.074	1.00
75_E	120_G	1.055	1.00
120_G	124_H	1.055	1.00
71_E	77_A	1.039	1.00
63_V	88_L	1.037	1.00
137_I	166_E	1.034	1.00
183_L	199_I	1.031	1.00
209_V	213_I	1.029	1.00
161_F	164_N	1.027	1.00
157_M	174_L	1.026	1.00
147_V	159_P	1.026	1.00
251_Q	266_S	1.019	1.00
90_K	94_S	1.019	1.00
161_F	168_L	1.018	1.00
142_F	146_K	1.013	1.00
214_Q	217_M	1.008	1.00
151_F	155_K	1.007	1.00
216_N	220_E	1.007	1.00
43_L	51_A	1.000	1.00
39_K	42_E	0.997	1.00
161_F	167_I	0.996	1.00
239_G	254_I	0.992	1.00
130_F	138_H	0.976	1.00
197_S	200_D	0.975	1.00
59_N	104_A	0.970	1.00
128_I	131_N	0.967	1.00
42_E	97_A	0.963	1.00
91_G	103_L	0.951	1.00
151_F	159_P	0.941	1.00
38_K	100_G	0.939	1.00
31_P	61_R	0.939	1.00
274_M	278_H	0.928	1.00
85_T	89_I	0.926	1.00
241_F	269_E	0.926	1.00
148_N	155_K	0.916	1.00
126_S	130_F	0.914	1.00
64_A	85_T	0.910	1.00
231_D	235_E	0.905	1.00
221_K	224_Q	0.900	1.00
252_R	255_A	0.898	1.00
44_M	55_L	0.898	1.00
232_R	268_I	0.897	1.00
112_E	118_T	0.880	1.00
252_R	262_R	0.868	0.99
219_L	223_K	0.864	0.99
62_L	105_T	0.864	0.99
87_G	91_G	0.862	0.99
65_H	68_K	0.862	0.99
81_I	84_G	0.860	0.99
148_N	151_F	0.858	0.99
236_V	258_L	0.857	0.99
37_E	41_L	0.856	0.99
162_V	165_N	0.854	0.99
52_R	92_I	0.854	0.99
94_S	110_C	0.851	0.99
232_R	236_V	0.846	0.99
35_S	39_K	0.846	0.99
44_M	47_G	0.845	0.99
123_I	128_I	0.844	0.99
68_K	77_A	0.842	0.99
40_Y	54_M	0.842	0.99
54_M	57_E	0.837	0.99
232_R	264_Y	0.829	0.99
203_K	206_N	0.828	0.99
60_L	63_V	0.827	0.99
211_D	214_Q	0.826	0.99
47_G	51_A	0.825	0.99
144_H	160_L	0.824	0.99
63_V	85_T	0.822	0.99
204_S	207_E	0.807	0.99
68_K	71_E	0.807	0.99
64_A	77_A	0.806	0.99
141_N	144_H	0.802	0.99
147_V	160_L	0.802	0.99
110_C	266_S	0.801	0.99
131_N	134_G	0.797	0.99
240_R	254_I	0.797	0.99
261_S	264_Y	0.797	0.99
251_Q	262_R	0.796	0.99
152_F	155_K	0.795	0.99
226_I	238_V	0.792	0.99
135_V	139_N	0.791	0.99
254_I	269_E	0.789	0.99
181_V	185_D	0.789	0.99
151_F	163_M	0.784	0.99
43_L	46_K	0.782	0.99
40_Y	51_A	0.780	0.99
144_H	174_L	0.764	0.99
120_G	126_S	0.759	0.99
223_K	238_V	0.759	0.99
113_N	122_C	0.754	0.99
224_Q	227_D	0.752	0.98
251_Q	267_R	0.751	0.98
55_L	92_I	0.748	0.98
216_N	219_L	0.748	0.98
225_Y	276_M	0.747	0.98
187_I	201_V	0.745	0.98
212_T	216_N	0.743	0.98
170_H	173_A	0.742	0.98
213_I	217_M	0.741	0.98
97_A	100_G	0.741	0.98
236_V	260_I	0.738	0.98
251_Q	264_Y	0.736	0.98
215_L	219_L	0.734	0.98
90_K	114_E	0.733	0.98
119_K	128_I	0.732	0.98
106_Y	110_C	0.731	0.98
30_Q	33_S	0.729	0.98
77_A	81_I	0.725	0.98
92_I	210_I	0.724	0.98
122_C	132_I	0.718	0.98
269_E	272_A	0.718	0.98
45_A	96_S	0.716	0.98
134_G	138_H	0.713	0.98
119_K	240_R	0.708	0.98
110_C	263_S	0.706	0.98
113_N	119_K	0.705	0.98
230_D	272_A	0.704	0.98
70_F	115_I	0.701	0.98
66_I	112_E	0.693	0.97
223_K	227_D	0.691	0.97
88_L	107_A	0.690	0.97
62_L	108_A	0.688	0.97
110_C	113_N	0.683	0.97
143_F	160_L	0.682	0.97
187_I	197_S	0.681	0.97
40_Y	44_M	0.679	0.97
113_N	132_I	0.674	0.97
120_G	123_I	0.674	0.97
137_I	140_G	0.670	0.97
253_E	256_K	0.668	0.97
86_I	89_I	0.667	0.97
64_A	78_E	0.664	0.97
220_E	224_Q	0.657	0.96
139_N	145_D	0.653	0.96
119_K	126_S	0.652	0.96
240_R	250_T	0.651	0.96
144_H	148_N	0.647	0.96
32_L	37_E	0.646	0.96
187_I	200_D	0.646	0.96
118_T	132_I	0.645	0.96
241_F	273_L	0.644	0.96
226_I	230_D	0.638	0.96
247_K	257_E	0.637	0.96
83_I	124_H	0.637	0.96
157_M	161_F	0.634	0.96
42_E	45_A	0.633	0.96
148_N	154_F	0.632	0.96
60_L	81_I	0.631	0.96
32_L	58_H	0.630	0.96
121_G	126_S	0.630	0.96
133_Y	136_R	0.629	0.95
164_N	171_L	0.624	0.95
214_Q	218_E	0.624	0.95
113_N	266_S	0.623	0.95
251_Q	269_E	0.622	0.95
119_K	250_T	0.622	0.95
34_S	37_E	0.621	0.95
63_V	115_I	0.620	0.95
108_A	261_S	0.620	0.95
125_P	128_I	0.619	0.95
36_E	40_Y	0.617	0.95
82_S	114_E	0.617	0.95
233_E	268_I	0.616	0.95
222_V	225_Y	0.614	0.95
41_L	92_I	0.612	0.95
60_L	64_A	0.607	0.95
228_I	281_Y	0.607	0.95
123_I	129_R	0.605	0.94
41_L	97_A	0.601	0.94
105_T	108_A	0.600	0.94
121_G	125_P	0.599	0.94
261_S	267_R	0.598	0.94
230_D	268_I	0.598	0.94
156_S	161_F	0.598	0.94
52_R	56_I	0.597	0.94
80_L	120_G	0.597	0.94
65_H	69_K	0.596	0.94
30_Q	36_E	0.594	0.94
114_E	120_G	0.592	0.94
225_Y	279_E	0.592	0.94
217_M	220_E	0.590	0.94
101_T	105_T	0.588	0.94
119_K	129_R	0.588	0.94
162_V	166_E	0.587	0.93
61_R	64_A	0.582	0.93
255_A	263_S	0.580	0.93
229_L	276_M	0.575	0.93
58_H	61_R	0.575	0.93
239_G	258_L	0.572	0.93
233_E	272_A	0.571	0.93
90_K	106_Y	0.570	0.92
64_A	67_V	0.567	0.92
262_R	267_R	0.566	0.92
197_S	201_V	0.565	0.92
49_E	52_R	0.564	0.92
130_F	134_G	0.564	0.92
44_M	51_A	0.562	0.92
240_R	262_R	0.560	0.92
121_G	128_I	0.559	0.92
187_I	193_G	0.557	0.92
144_H	147_V	0.556	0.92
113_N	242_G	0.552	0.91
153_I	156_S	0.550	0.91
255_A	262_R	0.549	0.91
159_P	162_V	0.549	0.91
82_S	119_K	0.549	0.91
260_I	264_Y	0.548	0.91
92_I	97_A	0.547	0.91
46_K	98_G	0.545	0.91
126_S	129_R	0.545	0.91
254_I	258_L	0.544	0.91
72_N	75_E	0.544	0.91
70_F	112_E	0.543	0.91
110_C	269_E	0.543	0.91
146_K	149_N	0.540	0.90
146_K	228_I	0.540	0.90
237_I	273_L	0.539	0.90
232_R	267_R	0.539	0.90
225_Y	228_I	0.538	0.90
34_S	41_L	0.537	0.90
131_N	135_V	0.537	0.90
66_I	111_I	0.534	0.90
182_S	186_P	0.532	0.90
188_G	201_V	0.532	0.90
123_I	126_S	0.532	0.90
37_E	58_H	0.530	0.90
43_L	47_G	0.527	0.89
240_R	251_Q	0.526	0.89
119_K	124_H	0.526	0.89
120_G	127_L	0.526	0.89
67_V	76_D	0.525	0.89
256_K	259_G	0.524	0.89
132_I	262_R	0.523	0.89
169_M	172_R	0.523	0.89
44_M	92_I	0.520	0.89
160_L	163_M	0.520	0.89
160_L	164_N	0.517	0.88
75_E	80_L	0.517	0.88
131_N	136_R	0.516	0.88
222_V	280_F	0.516	0.88
226_I	242_G	0.516	0.88
113_N	267_R	0.515	0.88
118_T	121_G	0.515	0.88
121_G	129_R	0.514	0.88
65_H	82_S	0.514	0.88
238_V	247_K	0.514	0.88
75_E	121_G	0.512	0.88
213_I	216_N	0.511	0.88
37_E	44_M	0.511	0.88
61_R	65_H	0.510	0.88
183_L	202_L	0.510	0.88
95_Y	101_T	0.505	0.87
198_L	201_V	0.503	0.87
62_L	65_H	0.503	0.87
128_I	180_D	0.503	0.87
121_G	254_I	0.502	0.87
118_T	123_I	0.501	0.87
186_P	204_S	0.500	0.87

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	0.8878	100	0.285	Contact Map
2a6hF	1	0.915	100	0.285	Contact Map
4yfkF	1	0.9728	100	0.372	Contact Map
1l0oC	1	0.1871	100	0.533	Contact Map
1rp3A	1	0.7721	100	0.565	Contact Map
3ugoA	1	0.3741	100	0.584	Contact Map
4nqwA	1	0.5034	99.9	0.665	Contact Map
4cxfA	1	0.5238	99.9	0.699	Contact Map
1or7A	2	0.6259	99.9	0.7	Contact Map
2q1zA	1	0.5952	99.9	0.706	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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