RPSB - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

RPSB - RNA polymerase sigma-B factor

UniProt:	P06574	Sequences: MTQPSKTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQVGMIGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELGPRIKMAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEADSDGSTVTILDIVGSQEDGYERVNQQLMLQSVLHVLSDREKQIIDLTYIQNKSQKETGDILGISQMHVSRLQRKAVKKLREALIEDPSMELM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	262 (231)
Sequences:	7399 (4380)
Seq/√Len:	288.1

ECOLI - RPOD RPOS RPOH FLIA
BACSU - RPSB SIGA RPSK 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
125_L	129_T	3.670	1.00
31_Q	72_K	3.515	1.00
128_E	141_F	3.323	1.00
131_R	137_E	3.292	1.00
211_K	215_D	2.969	1.00
124_Q	141_F	2.955	1.00
42_V	63_G	2.948	1.00
136_E	146_E	2.828	1.00
233_I	238_V	2.791	1.00
21_D	27_D	2.696	1.00
32_E	36_R	2.553	1.00
121_A	141_F	2.388	1.00
17_R	21_D	2.226	1.00
216_L	230_I	2.213	1.00
210_E	248_K	2.185	1.00
237_H	240_R	2.142	1.00
135_V	150_L	2.127	1.00
216_L	222_K	2.075	1.00
217_T	242_Q	2.047	1.00
205_V	252_A	2.007	1.00
145_S	148_E	1.998	1.00
212_Q	230_I	1.978	1.00
165_D	178_T	1.969	1.00
225_K	229_D	1.961	1.00
41_L	83_E	1.927	1.00
204_H	211_K	1.925	1.00
75_D	78_V	1.809	1.00
45_L	87_I	1.795	1.00
125_L	133_P	1.787	1.00
222_K	230_I	1.781	1.00
212_Q	216_L	1.748	1.00
213_I	241_L	1.743	1.00
124_Q	128_E	1.742	1.00
39_T	64_M	1.728	1.00
207_S	248_K	1.716	1.00
212_Q	231_L	1.714	1.00
62_V	97_F	1.688	1.00
81_S	84_A	1.645	1.00
213_I	245_A	1.642	1.00
236_M	239_S	1.630	1.00
33_T	37_V	1.626	1.00
231_L	238_V	1.611	1.00
138_I	149_V	1.608	1.00
136_E	140_E	1.601	1.00
135_V	153_M	1.589	1.00
28_E	32_E	1.586	1.00
121_A	124_Q	1.569	1.00
118_I	138_I	1.557	1.00
45_L	94_I	1.556	1.00
73_R	85_F	1.529	1.00
46_A	94_I	1.527	1.00
165_D	180_L	1.523	1.00
135_V	146_E	1.515	1.00
35_V	68_L	1.508	1.00
43_D	60_R	1.490	1.00
222_K	226_E	1.490	1.00
121_A	125_L	1.483	1.00
118_I	152_T	1.473	1.00
60_R	64_M	1.467	1.00
63_G	94_I	1.453	1.00
122_V	153_M	1.430	1.00
125_L	131_R	1.417	1.00
114_L	144_V	1.401	1.00
135_V	149_V	1.389	1.00
207_S	210_E	1.377	1.00
146_E	150_L	1.376	1.00
23_Q	77_V	1.361	1.00
125_L	141_F	1.351	1.00
237_H	241_L	1.344	1.00
71_I	82_F	1.331	1.00
139_A	149_V	1.314	1.00
46_A	60_R	1.310	1.00
210_E	244_K	1.308	1.00
82_F	86_A	1.286	1.00
121_A	142_L	1.284	1.00
113_E	117_R	1.276	1.00
23_Q	76_P	1.249	1.00
139_A	146_E	1.242	1.00
46_A	56_H	1.239	1.00
118_I	142_L	1.236	1.00
214_I	249_L	1.232	1.00
144_V	152_T	1.223	1.00
144_V	149_V	1.223	1.00
22_Y	26_Q	1.214	1.00
194_N	198_M	1.201	1.00
187_E	191_E	1.186	1.00
29_Q	32_E	1.178	1.00
218_Y	242_Q	1.165	1.00
19_I	22_Y	1.157	1.00
42_V	67_L	1.153	1.00
134_K	137_E	1.127	1.00
35_V	71_I	1.120	1.00
114_L	152_T	1.109	1.00
191_E	194_N	1.092	1.00
126_T	133_P	1.089	1.00
118_I	149_V	1.085	1.00
27_D	30_A	1.084	1.00
47_K	56_H	1.084	1.00
208_D	211_K	1.081	1.00
212_Q	215_D	1.073	1.00
241_L	245_A	1.073	1.00
70_A	86_A	1.063	1.00
216_L	227_T	1.053	1.00
20_S	77_V	1.053	1.00
224_Q	228_G	1.049	1.00
196_Q	200_Q	1.048	1.00
133_P	137_E	1.048	1.00
114_L	148_E	1.048	1.00
187_E	190_Y	1.034	1.00
209_R	241_L	1.029	1.00
236_M	240_R	1.026	1.00
19_I	23_Q	1.017	1.00
66_G	70_A	1.017	1.00
54_S	97_F	1.010	1.00
139_A	144_V	1.006	1.00
225_K	235_Q	0.997	1.00
21_D	26_Q	0.996	1.00
21_D	30_A	0.980	1.00
193_V	197_L	0.975	1.00
47_K	50_S	0.974	1.00
192_R	196_Q	0.973	1.00
120_M	124_Q	0.953	1.00
122_V	138_I	0.953	1.00
102_T	112_K	0.951	1.00
224_Q	236_M	0.946	1.00
125_L	138_I	0.944	1.00
224_Q	235_Q	0.943	1.00
29_Q	33_T	0.941	1.00
162_L	166_H	0.940	1.00
17_R	20_S	0.939	1.00
190_Y	194_N	0.939	1.00
210_E	241_L	0.938	1.00
247_K	251_E	0.928	1.00
164_V	180_L	0.925	1.00
198_M	201_S	0.925	1.00
50_S	56_H	0.913	1.00
34_L	71_I	0.907	1.00
60_R	63_G	0.905	1.00
21_D	33_T	0.903	1.00
21_D	25_K	0.901	1.00
224_Q	239_S	0.900	1.00
38_Y	83_E	0.898	1.00
121_A	138_I	0.898	1.00
209_R	237_H	0.898	1.00
45_L	91_I	0.889	1.00
91_I	95_K	0.889	1.00
126_T	132_S	0.886	1.00
129_T	133_P	0.884	1.00
209_R	213_I	0.883	1.00
174_G	182_I	0.883	1.00
150_L	154_E	0.882	1.00
69_G	73_R	0.881	1.00
42_V	64_M	0.881	1.00
33_T	36_R	0.880	1.00
67_L	86_A	0.874	1.00
20_S	76_P	0.874	1.00
18_L	33_T	0.872	1.00
18_L	30_A	0.872	1.00
43_D	64_M	0.868	1.00
69_G	93_E	0.864	1.00
129_T	137_E	0.863	1.00
85_F	89_T	0.862	1.00
217_T	227_T	0.856	1.00
208_D	212_Q	0.851	1.00
225_K	228_G	0.847	1.00
213_I	233_I	0.838	1.00
64_M	68_L	0.830	1.00
73_R	89_T	0.829	1.00
56_H	60_R	0.829	1.00
22_Y	34_L	0.825	1.00
215_D	220_Q	0.823	1.00
188_D	191_E	0.822	1.00
107_V	115_G	0.810	1.00
43_D	56_H	0.807	0.99
114_L	117_R	0.796	0.99
213_I	231_L	0.790	0.99
89_T	92_G	0.788	0.99
126_T	129_T	0.787	0.99
39_T	42_V	0.786	0.99
148_E	151_E	0.786	0.99
97_F	101_K	0.782	0.99
178_T	181_D	0.779	0.99
44_M	47_K	0.777	0.99
20_S	25_K	0.775	0.99
234_S	237_H	0.774	0.99
227_T	242_Q	0.771	0.99
118_I	153_M	0.771	0.99
96_R	100_D	0.770	0.99
203_L	215_D	0.763	0.99
129_T	141_F	0.761	0.99
49_Y	94_I	0.759	0.99
214_I	246_V	0.757	0.99
108_P	111_I	0.756	0.99
70_A	82_F	0.753	0.99
99_R	109_R	0.750	0.99
149_V	153_M	0.739	0.99
242_Q	245_A	0.736	0.99
201_S	204_H	0.734	0.99
34_L	38_Y	0.724	0.99
31_Q	71_I	0.723	0.99
183_V	186_Q	0.722	0.99
23_Q	75_D	0.721	0.99
179_I	182_I	0.720	0.99
112_K	116_P	0.719	0.99
80_K	84_A	0.718	0.99
65_I	68_L	0.717	0.99
22_Y	25_K	0.713	0.99
84_A	87_I	0.706	0.99
114_L	142_L	0.705	0.99
111_I	115_G	0.703	0.99
224_Q	240_R	0.703	0.99
217_T	224_Q	0.701	0.99
20_S	23_Q	0.699	0.99
202_V	249_L	0.698	0.99
209_R	233_I	0.698	0.99
115_G	152_T	0.696	0.98
86_A	90_I	0.694	0.98
103_W	107_V	0.693	0.98
117_R	120_M	0.692	0.98
179_I	183_V	0.691	0.98
168_I	182_I	0.691	0.98
130_Q	133_P	0.690	0.98
200_Q	215_D	0.689	0.98
44_M	48_K	0.685	0.98
125_L	137_E	0.679	0.98
92_G	96_R	0.677	0.98
41_L	87_I	0.670	0.98
40_N	43_D	0.670	0.98
168_I	178_T	0.664	0.98
37_V	40_N	0.664	0.98
76_P	79_G	0.663	0.98
197_L	201_S	0.659	0.98
92_G	99_R	0.654	0.98
26_Q	30_A	0.654	0.98
116_P	119_K	0.653	0.98
209_R	240_R	0.652	0.98
210_E	245_A	0.648	0.98
189_G	193_V	0.648	0.98
218_Y	246_V	0.647	0.98
224_Q	237_H	0.643	0.97
18_L	22_Y	0.642	0.97
152_T	155_M	0.640	0.97
193_V	196_Q	0.640	0.97
234_S	240_R	0.637	0.97
100_D	106_H	0.637	0.97
200_Q	204_H	0.636	0.97
202_V	252_A	0.636	0.97
202_V	245_A	0.634	0.97
169_E	182_I	0.633	0.97
66_G	94_I	0.633	0.97
220_Q	230_I	0.632	0.97
194_N	197_L	0.631	0.97
74_Y	78_V	0.629	0.97
151_E	155_M	0.629	0.97
226_E	229_D	0.629	0.97
118_I	144_V	0.629	0.97
89_T	236_M	0.628	0.97
89_T	239_S	0.627	0.97
169_E	172_S	0.624	0.97
217_T	235_Q	0.622	0.97
119_K	122_V	0.621	0.97
142_L	149_V	0.620	0.97
195_Q	202_V	0.619	0.97
68_L	71_I	0.615	0.97
151_E	154_E	0.613	0.97
207_S	245_A	0.613	0.97
139_A	142_L	0.612	0.97
115_G	156_G	0.612	0.97
69_G	72_K	0.611	0.97
190_Y	193_V	0.610	0.97
41_L	84_A	0.607	0.96
110_R	113_E	0.606	0.96
228_G	235_Q	0.605	0.96
43_D	46_A	0.605	0.96
169_E	173_D	0.602	0.96
180_L	183_V	0.602	0.96
74_Y	80_K	0.601	0.96
39_T	43_D	0.601	0.96
31_Q	35_V	0.601	0.96
39_T	60_R	0.600	0.96
111_I	152_T	0.598	0.96
137_E	141_F	0.598	0.96
28_E	31_Q	0.596	0.96
69_G	85_F	0.595	0.96
233_I	237_H	0.594	0.96
54_S	98_L	0.594	0.96
59_L	97_F	0.593	0.96
217_T	223_S	0.593	0.96
42_V	94_I	0.593	0.96
58_D	61_Q	0.591	0.96
246_V	250_R	0.589	0.96
224_Q	242_Q	0.589	0.96
103_W	112_K	0.587	0.96
63_G	90_I	0.587	0.96
23_Q	26_Q	0.586	0.96
227_T	231_L	0.584	0.96
134_K	138_I	0.582	0.96
122_V	132_S	0.581	0.95
207_S	241_L	0.580	0.95
43_D	57_E	0.578	0.95
163_S	166_H	0.578	0.95
46_A	59_L	0.574	0.95
22_Y	30_A	0.571	0.95
181_D	184_G	0.570	0.95
19_I	76_P	0.567	0.95
168_I	181_D	0.567	0.95
96_R	217_T	0.562	0.95
103_W	108_P	0.561	0.95
22_Y	27_D	0.559	0.94
105_V	161_A	0.559	0.94
89_T	96_R	0.554	0.94
235_Q	240_R	0.553	0.94
139_A	145_S	0.549	0.94
115_G	118_I	0.547	0.94
244_K	247_K	0.543	0.94
44_M	61_Q	0.543	0.94
117_R	121_A	0.535	0.93
202_V	205_V	0.534	0.93
154_E	157_K	0.534	0.93
206_L	249_L	0.533	0.93
54_S	59_L	0.533	0.93
133_P	138_I	0.528	0.93
228_G	236_M	0.528	0.93
135_V	142_L	0.526	0.92
162_L	165_D	0.526	0.92
121_A	129_T	0.526	0.92
92_G	239_S	0.525	0.92
71_I	76_P	0.525	0.92
140_E	143_D	0.525	0.92
199_L	202_V	0.524	0.92
43_D	47_K	0.524	0.92
149_V	152_T	0.523	0.92
62_V	101_K	0.522	0.92
164_V	183_V	0.521	0.92
149_V	155_M	0.517	0.92
178_T	182_I	0.517	0.92
229_D	232_G	0.515	0.92
19_I	71_I	0.510	0.91
42_V	71_I	0.510	0.91
66_G	86_A	0.508	0.91
61_Q	65_I	0.508	0.91
137_E	140_E	0.504	0.91
42_V	90_I	0.503	0.91
168_I	174_G	0.503	0.91
227_T	238_V	0.501	0.91
98_L	112_K	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
2a6hF	1	0.9618	100	0.228	Contact Map
1l9zH	1	0.9466	100	0.228	Contact Map
4yfkF	1	0.9771	100	0.287	Contact Map
1l0oC	1	0.2176	100	0.425	Contact Map
1rp3A	1	0.8702	100	0.477	Contact Map
3ugoA	1	0.3931	100	0.536	Contact Map
4nqwA	1	0.5649	99.9	0.618	Contact Map
4cxfA	1	0.5878	99.9	0.657	Contact Map
1or7A	2	0.7023	99.9	0.658	Contact Map
2q1zA	1	0.6679	99.9	0.661	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.

Page generated in 0.0086 seconds.