SIGW - BACSU - GREMLIN Contacts

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SIGW - ECF RNA polymerase sigma factor SigW

UniProt:	Q45585	Sequences: MEMMIKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFDINRKFSTWLYRIATNLTIDRIRKKKPDYYLDAEVAGTEGLTMYSQIVADGVLPEDAVVSLELSNTIQQKILKLPDKYRTVIVLKYIDELSLIEIGEILNIPVGTVKTRIHRGREALRKQLRDL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	187 (160)
Sequences:	41554 (30410)
Seq/√Len:	2404.2

ECOLI - RPOE FECI RPOH FLIA RPOS
BACSU - SIGW SIGY YLAC SIGX SIGV SIGM SIGZ RPSE RPSH RPSK RPSD RPSB RPSG RPSF SIGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_R	80_L	3.139	1.00
148_K	158_I	2.608	1.00
30_K	70_S	2.424	1.00
156_I	166_V	2.307	1.00
136_K	183_Q	2.276	1.00
141_Y	179_A	2.257	1.00
78_T	82_I	2.104	1.00
133_K	183_Q	2.072	1.00
35_C	77_A	2.053	1.00
153_L	161_I	2.006	1.00
52_A	77_A	2.000	1.00
140_K	172_R	1.955	1.00
167_G	170_K	1.856	1.00
147_L	161_I	1.799	1.00
68_K	71_T	1.740	1.00
59_N	62_S	1.731	1.00
21_A	25_D	1.718	1.00
43_H	46_E	1.699	1.00
165_P	168_T	1.662	1.00
22_D	26_I	1.648	1.00
83_D	86_R	1.639	1.00
138_P	141_Y	1.638	1.00
164_I	172_R	1.636	1.00
34_L	74_Y	1.632	1.00
80_L	83_D	1.598	1.00
141_Y	172_R	1.597	1.00
155_L	166_V	1.574	1.00
38_M	81_T	1.565	1.00
56_A	73_L	1.545	1.00
44_E	84_R	1.538	1.00
147_L	153_L	1.533	1.00
41_N	44_E	1.513	1.00
149_Y	177_R	1.504	1.00
168_T	172_R	1.497	1.00
174_H	178_E	1.494	1.00
154_S	157_E	1.486	1.00
168_T	171_T	1.475	1.00
155_L	173_I	1.474	1.00
155_L	170_K	1.473	1.00
30_K	74_Y	1.469	1.00
142_R	146_V	1.457	1.00
48_I	84_R	1.434	1.00
64_D	67_R	1.419	1.00
55_R	83_D	1.414	1.00
51_E	80_L	1.382	1.00
31_I	77_A	1.370	1.00
179_A	183_Q	1.365	1.00
36_Y	42_V	1.363	1.00
35_C	81_T	1.329	1.00
164_I	169_V	1.317	1.00
75_R	78_T	1.312	1.00
27_Y	70_S	1.268	1.00
79_N	82_I	1.266	1.00
144_V	173_I	1.257	1.00
148_K	173_I	1.254	1.00
144_V	176_G	1.245	1.00
70_S	74_Y	1.238	1.00
144_V	172_R	1.230	1.00
31_I	49_A	1.205	1.00
24_V	28_K	1.204	1.00
24_V	53_F	1.204	1.00
156_I	160_E	1.194	1.00
166_V	170_K	1.185	1.00
55_R	59_N	1.184	1.00
135_L	142_R	1.179	1.00
39_L	48_I	1.176	1.00
75_R	79_N	1.173	1.00
171_T	174_H	1.168	1.00
32_Y	42_V	1.166	1.00
122_V	125_E	1.163	1.00
153_L	157_E	1.145	1.00
34_L	78_T	1.141	1.00
27_Y	53_F	1.129	1.00
52_A	76_I	1.116	1.00
54_I	58_V	1.115	1.00
35_C	48_I	1.112	1.00
32_Y	36_Y	1.099	1.00
39_L	81_T	1.099	1.00
35_C	49_A	1.090	1.00
173_I	177_R	1.087	1.00
167_G	171_T	1.084	1.00
16_D	19_A	1.077	1.00
141_Y	176_G	1.073	1.00
148_K	155_L	1.072	1.00
42_V	46_E	1.064	1.00
171_T	175_R	1.063	1.00
149_Y	173_I	1.055	1.00
20_F	57_Y	1.054	1.00
31_I	52_A	1.051	1.00
48_I	80_L	1.044	1.00
63_F	66_N	1.026	1.00
27_Y	73_L	1.024	1.00
44_E	88_K	1.019	1.00
147_L	158_I	1.006	1.00
83_D	87_K	1.006	1.00
84_R	88_K	1.006	1.00
28_K	32_Y	1.005	1.00
52_A	80_L	1.003	1.00
82_I	85_I	0.996	1.00
80_L	84_R	0.995	1.00
133_K	136_K	0.995	1.00
141_Y	175_R	0.993	1.00
158_I	169_V	0.987	1.00
81_T	85_I	0.976	1.00
17_Q	21_A	0.973	1.00
118_E	122_V	0.968	1.00
32_Y	46_E	0.968	1.00
36_Y	45_A	0.960	1.00
48_I	81_T	0.952	1.00
127_S	131_Q	0.950	1.00
139_D	143_T	0.945	1.00
155_L	169_V	0.936	1.00
31_I	73_L	0.932	1.00
146_V	150_I	0.926	1.00
141_Y	144_V	0.919	1.00
133_K	180_L	0.915	1.00
28_K	49_A	0.907	1.00
23_I	69_F	0.902	1.00
144_V	164_I	0.897	1.00
146_V	151_D	0.895	1.00
33_Q	37_R	0.895	1.00
143_T	146_V	0.895	1.00
32_Y	45_A	0.895	1.00
140_K	164_I	0.890	1.00
145_I	149_Y	0.889	1.00
87_K	90_P	0.883	1.00
167_G	174_H	0.881	1.00
27_Y	30_K	0.879	1.00
35_C	45_A	0.876	1.00
32_Y	49_A	0.873	1.00
56_A	72_W	0.865	1.00
29_D	33_Q	0.850	1.00
67_R	71_T	0.849	1.00
178_E	182_K	0.844	1.00
55_R	58_V	0.840	1.00
72_W	76_I	0.832	1.00
18_D	21_A	0.819	1.00
133_K	184_L	0.818	1.00
164_I	168_T	0.802	1.00
63_F	67_R	0.800	1.00
20_F	61_D	0.797	1.00
159_G	166_V	0.790	1.00
75_R	82_I	0.790	1.00
143_T	162_L	0.778	1.00
143_T	147_L	0.774	1.00
88_K	91_D	0.763	1.00
30_K	34_L	0.762	1.00
22_D	25_D	0.762	1.00
49_A	53_F	0.742	1.00
129_T	132_Q	0.731	1.00
156_I	170_K	0.730	1.00
45_A	49_A	0.729	1.00
34_L	38_M	0.729	1.00
144_V	162_L	0.724	1.00
51_E	84_R	0.721	1.00
128_N	132_Q	0.717	1.00
157_E	160_E	0.717	1.00
126_L	129_T	0.716	1.00
50_Q	54_I	0.711	1.00
145_I	176_G	0.709	1.00
154_S	158_I	0.709	1.00
121_V	125_E	0.708	1.00
51_E	54_I	0.705	1.00
131_Q	135_L	0.702	1.00
158_I	162_L	0.692	1.00
74_Y	78_T	0.689	1.00
140_K	143_T	0.668	1.00
87_K	91_D	0.667	1.00
147_L	162_L	0.666	1.00
117_P	120_A	0.661	1.00
125_E	129_T	0.660	1.00
92_Y	95_D	0.658	1.00
89_K	93_Y	0.657	1.00
82_I	86_R	0.651	1.00
38_M	82_I	0.649	1.00
47_D	50_Q	0.641	1.00
91_D	95_D	0.638	1.00
125_E	128_N	0.634	1.00
56_A	76_I	0.628	1.00
177_R	181_R	0.626	1.00
175_R	178_E	0.626	1.00
25_D	28_K	0.624	1.00
120_A	124_L	0.621	1.00
84_R	87_K	0.620	1.00
28_K	53_F	0.618	1.00
34_L	81_T	0.616	1.00
57_Y	60_I	0.616	1.00
88_K	92_Y	0.616	1.00
121_V	124_L	0.616	1.00
85_I	89_K	0.615	1.00
124_L	127_S	0.608	1.00
95_D	99_A	0.606	1.00
145_I	180_L	0.606	1.00
77_A	81_T	0.604	1.00
52_A	56_A	0.603	1.00
175_R	179_A	0.602	1.00
60_I	69_F	0.593	1.00
147_L	151_D	0.592	1.00
39_L	84_R	0.590	1.00
30_K	33_Q	0.585	1.00
93_Y	97_E	0.584	1.00
63_F	71_T	0.582	1.00
139_D	142_R	0.579	1.00
143_T	161_I	0.578	1.00
172_R	176_G	0.571	1.00
18_D	22_D	0.566	1.00
39_L	45_A	0.564	1.00
63_F	68_K	0.564	1.00
159_G	162_L	0.561	1.00
36_Y	40_G	0.560	1.00
155_L	158_I	0.560	1.00
65_I	68_K	0.558	1.00
138_P	179_A	0.556	1.00
90_P	94_L	0.556	1.00
132_Q	136_K	0.552	1.00
96_A	99_A	0.551	1.00
134_I	146_V	0.546	1.00
159_G	169_V	0.545	1.00
41_N	46_E	0.542	1.00
94_L	97_E	0.542	1.00
131_Q	134_I	0.540	1.00
71_T	74_Y	0.540	1.00
116_L	119_D	0.535	1.00
94_L	98_V	0.534	1.00
38_M	78_T	0.534	1.00
137_L	176_G	0.533	1.00
179_A	182_K	0.533	1.00
119_D	123_S	0.531	1.00
56_A	69_F	0.529	1.00
48_I	77_A	0.522	1.00
158_I	173_I	0.520	1.00
123_S	126_L	0.517	1.00
131_Q	150_I	0.513	1.00
81_T	84_R	0.513	1.00
39_L	44_E	0.511	1.00
20_F	24_V	0.507	1.00
29_D	32_Y	0.505	1.00
134_I	145_I	0.504	1.00
89_K	92_Y	0.503	1.00
170_K	174_H	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
1or7A	2	0.9519	100	0.167	Contact Map
4cxfA	1	0.8182	100	0.177	Contact Map
4nqwA	1	0.7861	100	0.212	Contact Map
2q1zA	1	0.9251	100	0.216	Contact Map
4yfkF	1	1	100	0.235	Contact Map
1rp3A	1	0.9465	100	0.259	Contact Map
1l0oC	1	0.0856	100	0.259	Contact Map
2a6hF	1	0.9733	100	0.287	Contact Map
1l9zH	1	0.9572	100	0.295	Contact Map
2lfwA	1	0.7701	100	0.31	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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