YHAJ - ECOLI - GREMLIN Contacts

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YHAJ - Uncharacterized HTH-type transcriptional regulator YhaJ

UniProt:	P67660	Sequences: MAKERALTLEALRVMDAIDRRGSFAAAADELGRVPSALSYTMQKLEEELDVVLFDRSGHRTKFTNVGRMLLERGRVLLEAADKLTTDAEALARGWETHLTIVTEALVPTPAFFPLIDKLAAKANTQLAIITEVLAGAWERLEQGRADIVIAPDMHFRSSSEINSRKLYTLMNVYVAAPDHPIHQEPEPLSEVTRVKYRGIAVADTARERPVLTVQLLDKQPRLTVSTIEDKRQALLAGLGVATMPYPMVEKDIAEGRLRVVSPESTSEIDIIMAWRRDSMGEAKSWCLREIPKLFNGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12749
Length:	298 (279)
Sequences:	79586 (58100)
Seq/√Len:	3478.4

ECOLI - YHAJ YAHB XAPR YEEY LEUO LYSR TDCA YDHB TTDR YBDO OXYR ALLS NHAR DMLR YBHD CYSB YDCI PGRR ICIA ILVY DSDC CYNR HCAR YNEJ YAFC YJIE CBL YFER YBEF NAC AAER ABGR YHJC YIDZ PERR YFIE YIAU YNFL YCAN YEIE METR GCVA LRHA YGFI HDFR
BACSU - CYSL YVBU YWBI YCGK ALSR GLTC CITR YWQM YYBE BSDA GLTR YXJO YTLI YUST YKUM YOFA YOAU CZCR YRAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_V	80_A	3.571	1.00
21_R	30_E	3.351	1.00
165_R	292_P	2.619	1.00
102_V	146_A	2.479	1.00
73_R	87_D	2.413	1.00
17_A	30_E	2.263	1.00
180_H	197_Y	2.235	1.00
235_L	242_A	2.227	1.00
169_T	270_D	2.209	1.00
98_H	128_A	2.171	1.00
166_K	169_T	2.148	1.00
171_M	246_Y	2.136	1.00
166_K	270_D	2.100	1.00
98_H	126_Q	2.078	1.00
51_V	66_V	2.057	1.00
26_A	29_D	2.055	1.00
14_V	41_T	2.029	1.00
20_R	75_R	2.001	1.00
190_S	193_T	2.001	1.00
169_T	268_E	1.981	1.00
118_K	290_E	1.975	1.00
16_D	75_R	1.960	1.00
73_R	80_A	1.957	1.00
236_L	257_R	1.952	1.00
100_T	128_A	1.936	1.00
16_D	71_L	1.929	1.00
232_R	252_D	1.911	1.00
17_A	20_R	1.903	1.00
16_D	20_R	1.901	1.00
17_A	21_R	1.877	1.00
173_V	246_Y	1.870	1.00
19_D	63_F	1.866	1.00
14_V	38_L	1.855	1.00
176_A	261_V	1.854	1.00
77_L	81_A	1.843	1.00
200_I	240_G	1.834	1.00
71_L	75_R	1.803	1.00
24_F	42_M	1.743	1.00
55_D	62_K	1.720	1.00
236_L	252_D	1.716	1.00
137_A	149_V	1.706	1.00
70_L	84_L	1.684	1.00
173_V	260_V	1.678	1.00
69_M	87_D	1.665	1.00
164_S	272_I	1.663	1.00
140_R	145_R	1.626	1.00
19_D	71_L	1.598	1.00
119_L	287_C	1.584	1.00
21_R	26_A	1.565	1.00
20_R	30_E	1.560	1.00
198_R	222_R	1.557	1.00
16_D	74_G	1.554	1.00
163_N	277_R	1.537	1.00
15_M	71_L	1.512	1.00
14_V	33_R	1.499	1.00
11_A	41_T	1.498	1.00
139_E	143_Q	1.498	1.00
11_A	48_E	1.475	1.00
119_L	125_T	1.467	1.00
185_E	193_T	1.466	1.00
165_R	275_W	1.464	1.00
212_L	216_L	1.462	1.00
25_A	35_P	1.461	1.00
73_R	76_V	1.455	1.00
23_S	26_A	1.440	1.00
94_G	124_N	1.440	1.00
52_V	55_D	1.427	1.00
11_A	44_K	1.426	1.00
34_V	37_A	1.424	1.00
8_T	11_A	1.424	1.00
65_N	68_R	1.413	1.00
280_M	284_K	1.403	1.00
163_N	275_W	1.403	1.00
17_A	31_L	1.397	1.00
151_A	274_A	1.396	1.00
153_D	272_I	1.385	1.00
288_L	292_P	1.383	1.00
16_D	78_L	1.378	1.00
73_R	83_K	1.372	1.00
109_T	229_E	1.372	1.00
275_W	288_L	1.366	1.00
77_L	84_L	1.354	1.00
178_P	257_R	1.335	1.00
100_T	130_I	1.326	1.00
96_E	124_N	1.325	1.00
140_R	146_A	1.312	1.00
286_W	289_R	1.307	1.00
273_M	288_L	1.307	1.00
209_R	216_L	1.298	1.00
57_S	62_K	1.297	1.00
142_E	161_E	1.295	1.00
141_L	149_V	1.295	1.00
9_L	81_A	1.291	1.00
118_K	121_A	1.286	1.00
80_A	83_K	1.280	1.00
170_L	247_P	1.276	1.00
70_L	85_T	1.270	1.00
148_I	284_K	1.253	1.00
148_I	273_M	1.252	1.00
121_A	290_E	1.249	1.00
176_A	241_V	1.243	1.00
231_K	242_A	1.241	1.00
209_R	213_T	1.238	1.00
197_Y	241_V	1.232	1.00
72_E	76_V	1.229	1.00
48_E	85_T	1.228	1.00
73_R	84_L	1.209	1.00
233_Q	236_L	1.207	1.00
178_P	259_R	1.203	1.00
246_Y	250_E	1.188	1.00
69_M	72_E	1.182	1.00
246_Y	260_V	1.171	1.00
117_D	120_A	1.168	1.00
166_K	272_I	1.168	1.00
15_M	54_F	1.167	1.00
68_R	72_E	1.161	1.00
43_Q	47_E	1.158	1.00
33_R	37_A	1.155	1.00
164_S	274_A	1.144	1.00
250_E	254_A	1.143	1.00
252_D	257_R	1.140	1.00
176_A	180_H	1.136	1.00
15_M	19_D	1.134	1.00
40_Y	44_K	1.119	1.00
117_D	237_A	1.113	1.00
40_Y	43_Q	1.111	1.00
128_A	224_T	1.096	1.00
180_H	183_H	1.093	1.00
122_K	286_W	1.093	1.00
276_R	279_S	1.089	1.00
15_M	53_L	1.087	1.00
76_V	83_K	1.075	1.00
289_R	292_P	1.071	1.00
39_S	43_Q	1.071	1.00
99_L	287_C	1.070	1.00
24_F	61_T	1.065	1.00
175_V	260_V	1.064	1.00
69_M	73_R	1.064	1.00
188_P	264_E	1.062	1.00
108_P	131_T	1.060	1.00
18_I	27_A	1.059	1.00
12_L	74_G	1.059	1.00
17_A	27_A	1.054	1.00
10_E	13_R	1.048	1.00
77_L	80_A	1.047	1.00
114_P	237_A	1.046	1.00
198_R	220_Q	1.045	1.00
119_L	290_E	1.040	1.00
285_S	289_R	1.035	1.00
225_V	231_K	1.033	1.00
41_T	44_K	1.031	1.00
189_L	193_T	1.030	1.00
115_L	291_I	1.028	1.00
260_V	263_P	1.025	1.00
200_I	231_K	1.023	1.00
13_R	82_D	1.023	1.00
142_E	159_S	1.018	1.00
165_R	288_L	1.017	1.00
191_E	265_S	1.014	1.00
233_Q	237_A	1.012	1.00
232_R	236_L	1.003	1.00
212_L	217_L	1.002	1.00
177_A	238_G	1.000	1.00
63_F	67_G	0.989	1.00
85_T	89_E	0.988	1.00
171_M	268_E	0.978	1.00
119_L	122_K	0.978	1.00
251_K	255_E	0.974	1.00
82_D	85_T	0.966	1.00
79_E	83_K	0.961	1.00
130_I	140_R	0.957	1.00
175_V	249_V	0.956	1.00
174_Y	241_V	0.955	1.00
14_V	31_L	0.954	1.00
33_R	38_L	0.952	1.00
19_D	54_F	0.952	1.00
102_V	137_A	0.951	1.00
70_L	74_G	0.939	1.00
18_I	24_F	0.934	1.00
82_D	86_T	0.933	1.00
290_E	293_K	0.931	1.00
15_M	63_F	0.927	1.00
225_V	234_A	0.924	1.00
140_R	143_Q	0.922	1.00
201_A	221_P	0.922	1.00
44_K	47_E	0.916	1.00
27_A	38_L	0.915	1.00
281_G	284_K	0.911	1.00
176_A	182_I	0.909	1.00
213_T	216_L	0.905	1.00
121_A	293_K	0.899	1.00
15_M	45_L	0.897	1.00
207_R	210_P	0.892	1.00
115_L	290_E	0.891	1.00
69_M	91_L	0.881	1.00
51_V	88_A	0.880	1.00
26_A	30_E	0.880	1.00
54_F	61_T	0.880	1.00
105_A	227_T	0.879	1.00
19_D	67_G	0.872	1.00
146_A	149_V	0.866	1.00
102_V	151_A	0.864	1.00
72_E	75_R	0.862	1.00
126_Q	220_Q	0.861	1.00
153_D	270_D	0.859	1.00
199_G	219_K	0.851	1.00
249_V	252_D	0.850	1.00
163_N	166_K	0.847	1.00
76_V	79_E	0.845	1.00
210_P	213_T	0.844	1.00
22_G	62_K	0.843	1.00
195_V	217_L	0.840	1.00
193_T	196_K	0.837	1.00
10_E	41_T	0.837	1.00
161_E	277_R	0.835	1.00
25_A	29_D	0.833	1.00
31_L	38_L	0.829	1.00
211_V	215_Q	0.828	1.00
183_H	259_R	0.827	1.00
101_I	148_I	0.823	1.00
162_I	274_A	0.820	1.00
138_W	142_E	0.818	1.00
66_V	91_L	0.817	1.00
208_E	211_V	0.816	1.00
125_T	283_A	0.812	1.00
180_H	198_R	0.810	1.00
210_P	214_V	0.810	1.00
198_R	221_P	0.805	1.00
9_L	78_L	0.805	1.00
66_V	88_A	0.805	1.00
57_S	60_R	0.804	1.00
15_M	70_L	0.803	1.00
289_R	293_K	0.801	1.00
175_V	242_A	0.798	1.00
130_I	146_A	0.798	1.00
102_V	149_V	0.797	1.00
179_D	183_H	0.797	1.00
280_M	285_S	0.792	1.00
81_A	85_T	0.788	1.00
117_D	239_L	0.785	1.00
43_Q	52_V	0.783	1.00
22_G	68_R	0.780	1.00
177_A	180_H	0.779	1.00
208_E	212_L	0.778	1.00
97_T	283_A	0.776	1.00
252_D	255_E	0.774	1.00
35_P	39_S	0.774	1.00
253_I	256_G	0.773	1.00
19_D	22_G	0.772	1.00
177_A	239_L	0.771	1.00
20_R	71_L	0.770	1.00
66_V	69_M	0.768	1.00
80_A	84_L	0.767	1.00
136_G	139_E	0.766	1.00
192_V	195_V	0.765	1.00
83_K	87_D	0.761	1.00
21_R	27_A	0.760	1.00
22_G	60_R	0.759	1.00
18_I	42_M	0.757	1.00
81_A	84_L	0.757	1.00
190_S	264_E	0.754	1.00
234_A	239_L	0.754	1.00
171_M	262_S	0.751	1.00
207_R	216_L	0.750	1.00
97_T	125_T	0.748	1.00
18_I	54_F	0.748	1.00
148_I	287_C	0.744	1.00
11_A	14_V	0.738	1.00
282_E	286_W	0.734	1.00
142_E	162_I	0.733	1.00
24_F	38_L	0.733	1.00
249_V	253_I	0.727	1.00
175_V	253_I	0.726	1.00
55_D	64_T	0.723	1.00
154_M	157_R	0.719	1.00
74_G	77_L	0.715	1.00
175_V	244_M	0.714	1.00
13_R	17_A	0.714	1.00
176_A	259_R	0.714	1.00
84_L	88_A	0.711	1.00
103_T	108_P	0.709	1.00
95_W	122_K	0.709	1.00
18_I	38_L	0.708	1.00
75_R	79_E	0.705	1.00
119_L	286_W	0.704	1.00
89_E	92_A	0.700	1.00
245_P	248_M	0.698	1.00
121_A	286_W	0.688	1.00
190_S	265_S	0.687	1.00
62_K	68_R	0.685	1.00
63_F	68_R	0.684	1.00
236_L	255_E	0.680	1.00
100_T	146_A	0.679	1.00
147_D	284_K	0.678	1.00
286_W	290_E	0.677	1.00
66_V	70_L	0.677	1.00
185_E	198_R	0.675	1.00
227_T	230_D	0.675	1.00
65_N	69_M	0.674	1.00
68_R	71_L	0.673	1.00
182_I	185_E	0.672	1.00
180_H	185_E	0.671	1.00
144_G	276_R	0.669	1.00
55_D	60_R	0.668	1.00
202_V	231_K	0.667	1.00
37_A	41_T	0.664	1.00
253_I	260_V	0.664	1.00
79_E	82_D	0.659	1.00
188_P	262_S	0.657	1.00
46_E	51_V	0.656	1.00
223_L	234_A	0.650	1.00
118_K	293_K	0.646	1.00
70_L	88_A	0.645	1.00
196_K	220_Q	0.644	1.00
100_T	147_D	0.643	1.00
203_A	224_T	0.642	1.00
209_R	212_L	0.641	1.00
46_E	56_R	0.640	1.00
13_R	16_D	0.635	1.00
10_E	44_K	0.635	1.00
179_D	238_G	0.633	1.00
83_K	86_T	0.632	1.00
199_G	241_V	0.632	1.00
182_I	197_Y	0.632	1.00
99_L	283_A	0.631	1.00
179_D	259_R	0.629	1.00
126_Q	224_T	0.627	1.00
74_G	78_L	0.624	1.00
150_I	291_I	0.624	1.00
251_K	254_A	0.623	1.00
29_D	32_G	0.619	1.00
73_R	77_L	0.617	1.00
42_M	46_E	0.616	1.00
103_T	112_F	0.615	1.00
171_M	266_T	0.614	1.00
109_T	233_Q	0.612	1.00
27_A	31_L	0.612	1.00
131_T	226_S	0.607	1.00
282_E	285_S	0.602	1.00
24_F	60_R	0.601	1.00
8_T	48_E	0.597	1.00
174_Y	194_R	0.596	1.00
114_P	117_D	0.594	1.00
112_F	115_L	0.593	1.00
136_G	140_R	0.591	1.00
152_P	269_I	0.590	1.00
174_Y	243_T	0.590	1.00
18_I	23_S	0.590	1.00
86_T	90_A	0.588	1.00
141_L	274_A	0.586	1.00
212_L	215_Q	0.584	1.00
168_Y	271_I	0.582	1.00
131_T	227_T	0.581	1.00
208_E	216_L	0.581	1.00
99_L	148_I	0.579	1.00
13_R	78_L	0.578	1.00
69_M	88_A	0.576	1.00
36_S	40_Y	0.575	1.00
203_A	226_S	0.573	1.00
96_E	126_Q	0.573	1.00
148_I	288_L	0.572	1.00
275_W	285_S	0.568	1.00
287_C	291_I	0.567	1.00
185_E	188_P	0.567	1.00
178_P	256_G	0.567	1.00
49_L	70_L	0.566	1.00
211_V	214_V	0.566	1.00
49_L	88_A	0.565	1.00
63_F	71_L	0.565	1.00
37_A	40_Y	0.563	1.00
10_E	14_V	0.558	1.00
172_N	243_T	0.556	1.00
54_F	63_F	0.555	1.00
234_A	240_G	0.555	1.00
163_N	278_D	0.554	1.00
204_D	224_T	0.553	1.00
15_M	67_G	0.552	1.00
170_L	269_I	0.551	1.00
114_P	118_K	0.550	1.00
34_V	40_Y	0.549	1.00
231_K	235_L	0.547	1.00
180_H	241_V	0.546	1.00
51_V	55_D	0.546	1.00
141_L	162_I	0.544	1.00
174_Y	199_G	0.544	1.00
225_V	230_D	0.543	1.00
97_T	124_N	0.543	1.00
137_A	144_G	0.542	1.00
263_P	266_T	0.539	1.00
97_T	122_K	0.537	1.00
90_A	95_W	0.536	1.00
78_L	82_D	0.535	1.00
116_I	127_L	0.535	1.00
176_A	183_H	0.533	1.00
49_L	52_V	0.533	1.00
167_L	273_M	0.532	1.00
195_V	218_D	0.529	1.00
24_F	35_P	0.529	1.00
244_M	249_V	0.529	1.00
122_K	125_T	0.528	1.00
207_R	211_V	0.528	1.00
153_D	164_S	0.526	1.00
14_V	42_M	0.519	1.00
107_V	111_A	0.518	1.00
139_E	145_R	0.516	1.00
72_E	87_D	0.514	1.00
102_V	130_I	0.514	1.00
188_P	193_T	0.511	1.00
24_F	56_R	0.509	1.00
228_I	245_P	0.509	1.00
78_L	81_A	0.509	1.00
19_D	68_R	0.509	1.00
284_K	288_L	0.508	1.00
52_V	66_V	0.505	1.00
109_T	227_T	0.505	1.00
14_V	27_A	0.505	1.00
73_R	88_A	0.501	1.00
150_I	273_M	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
2esnA	3	0.9799	100	0.124	Contact Map
1ixcA	4	0.9597	100	0.128	Contact Map
1uthA	2	0.7282	100	0.128	Contact Map
2h98A	2	0.6644	100	0.13	Contact Map
3fzvA	4	0.9497	100	0.133	Contact Map
2h9bA	2	0.6644	100	0.134	Contact Map
3fxqA	3	0.9664	100	0.141	Contact Map
1al3A	1	0.6846	100	0.143	Contact Map
4x6gA	4	0.9832	100	0.143	Contact Map
3szpA	3	0.953	100	0.152	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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