YPLP - BACSU - GREMLIN Contacts

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YPLP - Putative sigma L-dependent transcriptional regulator YplP

UniProt:	P54156	Sequences: MNSAPKLNTFQHLIGEHQTFLEAKRIAKQFSLSELPVLITGKIGTGKNHFAHAIHLESSRSNEPFISVNCSTHSEETLIHELFGPNGNTGVFQKAVRGTLFLDDVWRMPASVQAQLLKALDSDTEKPRMICASADRSVEHTFRQDLFYRLNILTLTLPELSERKSDIPLLTQHFLSNSGQQLLIDPSVFPVLEKHAFEGNVRELKNAADYMAAVSSGGTIQPYDLPPYIRGTIDGKTSKKKAKLLTLMEKAEFLFILETIKVLNEKGEPASRRIISEHSKNTQTSLTPQQVRSRLDYLEKKDYVTKSRGRAGTKITFEGLSFIETLKNQMI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	331 (278)
Sequences:	28723 (19372)
Seq/√Len:	1161.8

ECOLI - DHAR RTCR YGEV TYRR PRPR ATOC GLRR NTRC NORR ZRAR HYFR FHLA PSPF RUVB RARA
BACSU - YPLP YQIR ACOR ROCR LEVR RUVB YRVN
HALSA - RFCS
SULSO - Q97V06 Q97W74

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
263_L	273_R	4.217	1.00
91_V	126_K	3.171	1.00
75_E	111_S	2.961	1.00
42_K	161_S	2.910	1.00
101_F	132_A	2.609	1.00
253_F	257_L	2.473	1.00
177_N	205_K	2.471	1.00
29_Q	216_S	2.447	1.00
93_Q	127_P	2.314	1.00
27_A	50_F	2.300	1.00
92_F	119_A	2.226	1.00
168_P	189_F	2.206	1.00
168_P	193_E	2.114	1.00
263_L	270_A	2.110	1.00
71_S	114_A	2.078	1.00
79_I	115_Q	2.029	1.00
171_T	208_A	2.016	1.00
107_R	135_D	1.991	1.00
255_F	259_T	1.989	1.00
259_T	263_L	1.958	1.00
197_F	207_A	1.932	1.00
172_Q	189_F	1.926	1.00
28_K	57_E	1.907	1.00
195_H	198_E	1.905	1.00
40_T	156_T	1.856	1.00
164_K	168_P	1.839	1.00
40_T	154_T	1.828	1.00
89_T	93_Q	1.810	1.00
266_K	269_P	1.809	1.00
50_F	157_L	1.794	1.00
16_E	169_L	1.757	1.00
78_L	112_V	1.738	1.00
279_S	283_Q	1.728	1.00
258_E	262_V	1.709	1.00
17_H	165_S	1.707	1.00
262_V	273_R	1.698	1.00
183_L	219_T	1.695	1.00
257_L	261_K	1.659	1.00
190_P	194_K	1.647	1.00
35_L	209_D	1.624	1.00
251_A	255_F	1.620	1.00
30_F	153_L	1.595	1.00
185_D	221_Q	1.575	1.00
53_A	57_E	1.565	1.00
173_H	177_N	1.564	1.00
269_P	273_R	1.553	1.00
269_P	272_R	1.548	1.00
243_K	246_T	1.544	1.00
260_I	270_A	1.538	1.00
279_S	282_T	1.536	1.00
185_D	188_V	1.531	1.00
168_P	172_Q	1.516	1.00
15_G	20_F	1.503	1.00
268_E	272_R	1.495	1.00
121_D	205_K	1.494	1.00
278_H	282_T	1.486	1.00
171_T	184_I	1.474	1.00
86_N	127_P	1.472	1.00
259_T	270_A	1.468	1.00
48_N	118_K	1.459	1.00
63_E	97_R	1.456	1.00
221_Q	224_D	1.438	1.00
215_S	224_D	1.416	1.00
277_E	280_K	1.411	1.00
164_K	167_I	1.411	1.00
187_S	222_P	1.408	1.00
52_H	67_S	1.388	1.00
13_L	20_F	1.387	1.00
191_V	222_P	1.380	1.00
12_H	56_L	1.369	1.00
23_A	50_F	1.366	1.00
14_I	173_H	1.360	1.00
174_F	205_K	1.355	1.00
195_H	203_E	1.344	1.00
15_G	24_K	1.339	1.00
75_E	109_P	1.336	1.00
188_V	192_L	1.324	1.00
244_L	248_M	1.324	1.00
252_E	284_T	1.315	1.00
248_M	251_A	1.302	1.00
267_G	282_T	1.299	1.00
92_F	100_L	1.298	1.00
247_L	251_A	1.294	1.00
169_L	172_Q	1.287	1.00
189_F	193_E	1.286	1.00
20_F	24_K	1.272	1.00
254_L	258_E	1.261	1.00
89_T	94_K	1.257	1.00
22_E	25_R	1.245	1.00
282_T	286_L	1.239	1.00
178_S	212_A	1.238	1.00
164_K	196_A	1.234	1.00
23_A	155_L	1.231	1.00
244_L	247_L	1.226	1.00
184_I	208_A	1.215	1.00
261_K	265_E	1.214	1.00
271_S	275_I	1.213	1.00
247_L	250_K	1.210	1.00
181_Q	209_D	1.209	1.00
280_K	284_T	1.209	1.00
35_L	213_A	1.207	1.00
176_S	180_Q	1.200	1.00
165_S	193_E	1.196	1.00
188_V	222_P	1.192	1.00
25_R	28_K	1.185	1.00
106_W	133_S	1.185	1.00
175_L	184_I	1.184	1.00
249_E	287_T	1.182	1.00
32_L	59_S	1.181	1.00
254_L	257_L	1.179	1.00
131_C	150_L	1.176	1.00
22_E	26_I	1.173	1.00
10_F	53_A	1.172	1.00
19_T	162_E	1.169	1.00
188_V	220_I	1.164	1.00
34_E	181_Q	1.163	1.00
185_D	219_T	1.162	1.00
167_I	193_E	1.161	1.00
170_L	174_F	1.159	1.00
34_E	60_R	1.159	1.00
93_Q	125_E	1.156	1.00
71_S	115_Q	1.154	1.00
277_E	283_Q	1.151	1.00
91_V	94_K	1.143	1.00
80_H	85_P	1.138	1.00
178_S	208_A	1.135	1.00
164_K	193_E	1.130	1.00
19_T	22_E	1.124	1.00
35_L	152_I	1.120	1.00
81_E	85_P	1.114	1.00
283_Q	287_T	1.102	1.00
190_P	193_E	1.100	1.00
48_N	67_S	1.100	1.00
108_M	112_V	1.088	1.00
45_T	157_L	1.087	1.00
211_M	215_S	1.086	1.00
138_V	142_F	1.080	1.00
258_E	261_K	1.077	1.00
247_L	255_F	1.073	1.00
267_G	278_H	1.072	1.00
81_E	88_N	1.072	1.00
156_T	162_E	1.067	1.00
27_A	53_A	1.067	1.00
248_M	255_F	1.065	1.00
65_F	98_G	1.061	1.00
191_V	194_K	1.057	1.00
284_T	288_P	1.057	1.00
36_P	123_D	1.052	1.00
178_S	205_K	1.050	1.00
268_E	278_H	1.039	1.00
282_T	285_S	1.036	1.00
205_K	209_D	1.032	1.00
119_A	125_E	1.031	1.00
120_L	129_M	1.028	1.00
179_G	212_A	1.027	1.00
34_E	59_S	1.027	1.00
78_L	82_L	1.023	1.00
38_L	131_C	1.022	1.00
186_P	189_F	1.020	1.00
178_S	182_L	1.020	1.00
52_H	56_L	1.019	1.00
21_L	24_K	1.010	1.00
246_T	250_K	1.005	1.00
37_V	54_I	1.004	1.00
168_P	171_T	1.001	1.00
26_I	214_V	0.997	1.00
259_T	274_I	0.997	1.00
249_E	253_F	0.977	1.00
24_K	27_A	0.974	1.00
250_K	254_L	0.967	1.00
259_T	262_V	0.967	1.00
210_Y	214_V	0.963	1.00
259_T	273_R	0.961	1.00
244_L	251_A	0.958	1.00
35_L	182_L	0.955	1.00
67_S	118_K	0.953	1.00
256_I	259_T	0.950	1.00
226_P	230_R	0.947	1.00
20_F	23_A	0.943	1.00
13_L	50_F	0.940	1.00
159_E	162_E	0.933	1.00
39_I	51_A	0.927	1.00
151_N	154_T	0.927	1.00
23_A	27_A	0.926	1.00
217_G	221_Q	0.924	1.00
280_K	283_Q	0.922	1.00
51_A	65_F	0.919	1.00
184_I	188_V	0.916	1.00
207_A	211_M	0.915	1.00
18_Q	22_E	0.913	1.00
260_I	267_G	0.910	1.00
55_H	99_T	0.910	1.00
157_L	160_L	0.907	1.00
42_K	45_T	0.903	1.00
88_N	91_V	0.900	1.00
13_L	49_H	0.894	1.00
217_G	224_D	0.888	1.00
281_N	285_S	0.886	1.00
276_S	280_K	0.886	1.00
186_P	190_P	0.886	1.00
184_I	189_F	0.885	1.00
167_I	171_T	0.883	1.00
270_A	273_R	0.879	1.00
256_I	281_N	0.874	1.00
266_K	270_A	0.873	1.00
175_L	212_A	0.873	1.00
253_F	288_P	0.868	1.00
15_G	169_L	0.866	1.00
266_K	278_H	0.865	1.00
27_A	155_L	0.860	1.00
267_G	285_S	0.859	1.00
88_N	94_K	0.856	1.00
182_L	213_A	0.855	1.00
60_R	63_E	0.848	1.00
263_L	269_P	0.846	1.00
39_I	50_F	0.843	1.00
106_W	138_V	0.842	1.00
178_S	209_D	0.841	1.00
147_F	151_N	0.840	1.00
172_Q	176_S	0.838	1.00
267_G	279_S	0.836	1.00
270_A	281_N	0.830	1.00
174_F	178_S	0.828	1.00
16_E	21_L	0.826	1.00
99_T	130_I	0.826	1.00
187_S	221_Q	0.822	1.00
85_P	88_N	0.819	1.00
14_I	169_L	0.808	1.00
249_E	252_E	0.804	1.00
42_K	159_E	0.804	1.00
146_L	150_L	0.797	1.00
106_W	134_A	0.797	1.00
252_E	256_I	0.793	1.00
245_L	249_E	0.791	1.00
277_E	282_T	0.789	1.00
242_A	246_T	0.786	1.00
105_V	142_F	0.782	1.00
53_A	56_L	0.779	1.00
255_F	258_E	0.776	1.00
24_K	50_F	0.773	1.00
273_R	277_E	0.773	1.00
164_K	169_L	0.772	1.00
220_I	225_L	0.772	1.00
211_M	220_I	0.771	1.00
71_S	107_R	0.770	1.00
35_L	153_L	0.767	1.00
81_E	91_V	0.766	1.00
255_F	274_I	0.764	1.00
243_K	275_I	0.762	1.00
70_C	102_L	0.761	1.00
251_A	254_L	0.760	1.00
226_P	229_I	0.756	1.00
182_L	212_A	0.754	1.00
18_Q	21_L	0.752	1.00
208_A	211_M	0.751	1.00
256_I	260_I	0.750	1.00
164_K	194_K	0.747	1.00
177_N	181_Q	0.747	1.00
24_K	28_K	0.747	1.00
246_T	249_E	0.745	1.00
142_F	146_L	0.743	1.00
52_H	122_S	0.743	1.00
23_A	157_L	0.742	1.00
263_L	266_K	0.733	1.00
210_Y	213_A	0.732	1.00
68_V	91_V	0.731	1.00
260_I	263_L	0.730	1.00
36_P	131_C	0.729	1.00
275_I	278_H	0.728	1.00
78_L	108_M	0.728	1.00
283_Q	286_L	0.727	1.00
167_I	192_L	0.726	1.00
33_S	213_A	0.726	1.00
96_V	125_E	0.725	1.00
143_R	148_Y	0.724	1.00
171_T	204_L	0.723	1.00
106_W	135_D	0.722	1.00
267_G	271_S	0.719	1.00
140_H	143_R	0.716	1.00
26_I	153_L	0.716	1.00
152_I	206_N	0.712	1.00
13_L	24_K	0.711	1.00
285_S	288_P	0.709	1.00
118_K	122_S	0.708	1.00
260_I	265_E	0.707	1.00
38_L	105_V	0.706	1.00
26_I	29_Q	0.706	1.00
25_R	216_S	0.704	1.00
178_S	181_Q	0.703	1.00
241_K	244_L	0.700	1.00
156_T	159_E	0.698	1.00
10_F	27_A	0.686	1.00
270_A	274_I	0.686	1.00
25_R	29_Q	0.682	1.00
276_S	281_N	0.681	1.00
21_L	25_R	0.681	1.00
64_P	94_K	0.679	1.00
66_I	95_A	0.679	1.00
250_K	253_F	0.678	1.00
191_V	195_H	0.678	1.00
274_I	277_E	0.677	1.00
173_H	176_S	0.676	1.00
256_I	284_T	0.672	1.00
171_T	189_F	0.671	1.00
105_V	131_C	0.670	1.00
265_E	270_A	0.666	1.00
31_S	57_E	0.664	1.00
246_T	254_L	0.662	1.00
248_M	252_E	0.660	1.00
107_R	134_A	0.656	1.00
260_I	264_N	0.653	1.00
267_G	274_I	0.653	1.00
268_E	271_S	0.653	1.00
260_I	285_S	0.653	1.00
271_S	274_I	0.653	1.00
249_E	288_P	0.652	1.00
172_Q	183_L	0.652	1.00
188_V	191_V	0.652	1.00
265_E	269_P	0.650	1.00
279_S	286_L	0.647	1.00
100_L	129_M	0.647	1.00
219_T	222_P	0.646	1.00
17_H	166_D	0.643	1.00
135_D	141_T	0.640	1.00
169_L	173_H	0.639	1.00
156_T	160_L	0.639	1.00
267_G	281_N	0.638	1.00
256_I	270_A	0.638	1.00
256_I	274_I	0.636	1.00
232_T	235_G	0.634	1.00
76_E	79_I	0.633	1.00
281_N	284_T	0.631	1.00
27_A	54_I	0.630	1.00
257_L	260_I	0.628	1.00
10_F	56_L	0.627	1.00
92_F	129_M	0.624	1.00
39_I	157_L	0.619	1.00
69_N	107_R	0.619	1.00
73_H	91_V	0.618	1.00
265_E	285_S	0.616	1.00
34_E	182_L	0.614	1.00
151_N	210_Y	0.612	1.00
145_D	148_Y	0.611	1.00
175_L	179_G	0.609	1.00
67_S	124_T	0.609	1.00
27_A	57_E	0.606	1.00
29_Q	214_V	0.604	1.00
16_E	165_S	0.603	1.00
246_T	251_A	0.600	1.00
252_E	255_F	0.600	1.00
222_P	225_L	0.600	1.00
274_I	284_T	0.600	1.00
211_M	225_L	0.600	1.00
225_L	228_Y	0.599	1.00
268_E	282_T	0.598	1.00
274_I	281_N	0.591	1.00
174_F	208_A	0.591	1.00
244_L	255_F	0.589	1.00
277_E	281_N	0.587	1.00
263_L	267_G	0.586	1.00
74_S	77_T	0.586	1.00
159_E	166_D	0.586	1.00
158_P	163_R	0.581	1.00
15_G	21_L	0.581	1.00
271_S	281_N	0.580	1.00
171_T	175_L	0.578	1.00
245_L	248_M	0.577	1.00
212_A	215_S	0.576	1.00
10_F	24_K	0.576	1.00
154_T	210_Y	0.574	1.00
230_R	234_D	0.571	1.00
11_Q	56_L	0.571	1.00
170_L	201_V	0.570	1.00
228_Y	231_G	0.568	1.00
242_A	245_L	0.567	1.00
153_L	214_V	0.564	1.00
100_L	119_A	0.564	1.00
195_H	229_I	0.557	1.00
256_I	285_S	0.557	1.00
129_M	150_L	0.556	1.00
261_K	264_N	0.554	1.00
267_G	270_A	0.552	1.00
284_T	287_T	0.551	1.00
251_A	256_I	0.548	1.00
191_V	226_P	0.547	1.00
140_H	144_Q	0.546	1.00
12_H	52_H	0.546	1.00
216_S	224_D	0.545	1.00
20_F	50_F	0.544	1.00
91_V	95_A	0.539	1.00
112_V	115_Q	0.538	1.00
78_L	115_Q	0.538	1.00
160_L	193_E	0.538	1.00
252_E	288_P	0.534	1.00
43_I	144_Q	0.534	1.00
231_G	234_D	0.533	1.00
77_T	80_H	0.531	1.00
163_R	167_I	0.531	1.00
179_G	182_L	0.526	1.00
10_F	28_K	0.524	1.00
235_G	238_S	0.522	1.00
209_D	213_A	0.522	1.00
30_F	37_V	0.518	1.00
278_H	281_N	0.513	1.00
256_I	288_P	0.513	1.00
227_P	231_G	0.512	1.00
39_I	130_I	0.512	1.00
70_C	73_H	0.512	1.00
227_P	230_R	0.508	1.00
276_S	282_T	0.505	1.00
184_I	220_I	0.504	1.00
168_P	190_P	0.502	1.00
110_A	114_A	0.501	1.00
51_A	130_I	0.501	1.00
19_T	165_S	0.501	1.00
66_I	94_K	0.500	1.00
43_I	147_F	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
4l4uA	2	0.6858	100	0.257	Contact Map
1ojlA	3	0.8187	100	0.315	Contact Map
3dzdA	2	0.6647	100	0.419	Contact Map
4qhsA	3	0.6465	100	0.477	Contact Map
4qosA	1	0.6616	100	0.483	Contact Map
1qvrA	3	0.7221	100	0.484	Contact Map
1r6bX	1	0.7372	100	0.486	Contact Map
3pxiA	3	0.7039	100	0.496	Contact Map
3vkgA	2	0.9517	100	0.508	Contact Map
4d2uA	3	0.7281	100	0.509	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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