YKUM - BACSU - GREMLIN Contacts

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YKUM - Uncharacterized HTH-type transcriptional regulator YkuM

UniProt:	O34827	Sequences: MQLQELHMLVVLAEELNMRKAAERLFVSQPALSQRLQTIEKAWGTKIFLRSQKGLTVTPAGEKIIQFANDVTLEQERIRENIDELEGEIHGTLKLAVASIIGQHWLPKVLKTYVEKYPNAKISLITGWSSEMLKSLYEDQVHIGIIRGNPEWKGRKDYLMTDHLYLVDTEISCIEDIAHTERPFIQFKSDSTYFQEIQHWWHQKFKTSPKQTILVDQIETCKQMALHGIGYAILPSVTLQNEDKVNKMPLLDMKGHPIGRDTWLLGYEPAFELKQVQAFVQVIKDMLDQENPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	293 (278)
Sequences:	79587 (58313)
Seq/√Len:	3497.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_D	74_E	3.560	1.00
15_E	24_R	3.391	1.00
157_D	284_K	2.676	1.00
96_A	141_V	2.547	1.00
67_F	81_N	2.423	1.00
225_A	232_A	2.369	1.00
163_H	236_S	2.239	1.00
11_V	24_R	2.188	1.00
161_T	261_D	2.176	1.00
14_E	69_N	2.162	1.00
20_K	23_E	2.151	1.00
158_Y	161_T	2.145	1.00
92_T	123_S	2.145	1.00
92_T	121_K	2.101	1.00
158_Y	261_D	2.038	1.00
222_K	242_E	2.037	1.00
8_M	35_R	2.026	1.00
10_V	65_I	2.017	1.00
94_K	123_S	2.009	1.00
45_T	60_A	2.003	1.00
161_T	259_G	1.973	1.00
168_D	251_L	1.968	1.00
112_T	282_V	1.958	1.00
67_F	74_E	1.948	1.00
226_L	247_K	1.931	1.00
18_M	36_L	1.924	1.00
71_V	75_Q	1.916	1.00
11_V	14_E	1.912	1.00
10_V	69_N	1.902	1.00
8_M	32_L	1.897	1.00
13_A	57_V	1.892	1.00
10_V	14_E	1.865	1.00
11_V	15_E	1.857	1.00
226_L	242_E	1.857	1.00
65_I	69_N	1.824	1.00
165_Y	236_S	1.791	1.00
132_M	144_G	1.756	1.00
49_L	56_T	1.742	1.00
64_I	78_I	1.732	1.00
173_C	182_R	1.698	1.00
63_K	81_N	1.677	1.00
113_Y	279_F	1.672	1.00
185_I	230_G	1.662	1.00
165_Y	250_L	1.637	1.00
14_E	24_R	1.636	1.00
156_K	263_W	1.616	1.00
135_S	140_Q	1.615	1.00
9_L	65_I	1.609	1.00
13_A	65_I	1.588	1.00
8_M	27_V	1.580	1.00
15_E	20_K	1.566	1.00
10_V	68_A	1.564	1.00
113_Y	120_A	1.559	1.00
88_E	119_N	1.543	1.00
19_R	29_Q	1.536	1.00
183_P	212_T	1.533	1.00
59_P	62_E	1.532	1.00
134_K	138_E	1.529	1.00
5_E	35_R	1.521	1.00
155_R	268_E	1.485	1.00
28_S	31_A	1.473	1.00
5_E	38_T	1.470	1.00
5_E	42_A	1.467	1.00
46_K	49_L	1.455	1.00
10_V	72_T	1.451	1.00
194_F	198_Q	1.435	1.00
17_N	20_K	1.433	1.00
67_F	70_D	1.413	1.00
157_D	266_G	1.412	1.00
11_V	25_L	1.410	1.00
146_I	265_L	1.407	1.00
148_G	263_W	1.390	1.00
155_R	266_G	1.389	1.00
71_V	78_I	1.386	1.00
280_V	284_K	1.385	1.00
170_E	247_K	1.377	1.00
67_F	77_R	1.375	1.00
143_I	276_V	1.362	1.00
103_Q	219_E	1.358	1.00
264_L	280_V	1.337	1.00
266_G	280_V	1.336	1.00
112_T	116_K	1.334	1.00
90_H	119_N	1.333	1.00
94_K	125_I	1.325	1.00
136_L	144_G	1.321	1.00
272_E	276_V	1.319	1.00
127_G	131_E	1.314	1.00
42_A	79_R	1.308	1.00
278_A	281_Q	1.301	1.00
242_E	247_K	1.298	1.00
64_I	79_R	1.291	1.00
3_L	75_Q	1.277	1.00
221_C	232_A	1.275	1.00
162_D	237_V	1.271	1.00
143_I	264_L	1.270	1.00
114_V	212_T	1.262	1.00
51_S	56_T	1.260	1.00
135_S	141_V	1.257	1.00
240_Q	244_K	1.249	1.00
62_E	66_Q	1.243	1.00
37_Q	41_K	1.231	1.00
236_S	240_Q	1.230	1.00
74_E	77_R	1.228	1.00
201_W	207_T	1.220	1.00
236_S	250_L	1.217	1.00
223_Q	226_L	1.214	1.00
66_Q	70_D	1.210	1.00
116_K	282_V	1.209	1.00
9_L	48_F	1.195	1.00
63_K	66_Q	1.193	1.00
182_R	231_Y	1.193	1.00
67_F	78_I	1.185	1.00
112_T	115_E	1.174	1.00
111_K	115_E	1.173	1.00
93_L	279_F	1.160	1.00
158_Y	263_W	1.154	1.00
9_L	47_I	1.152	1.00
170_E	249_P	1.151	1.00
156_K	265_L	1.149	1.00
27_V	31_A	1.136	1.00
168_D	231_Y	1.135	1.00
33_S	37_Q	1.131	1.00
7_H	76_E	1.129	1.00
113_Y	282_V	1.128	1.00
9_L	13_A	1.128	1.00
34_Q	37_Q	1.118	1.00
111_K	227_H	1.117	1.00
123_S	214_L	1.105	1.00
12_L	21_A	1.102	1.00
34_Q	38_T	1.102	1.00
215_V	221_C	1.096	1.00
167_V	250_L	1.095	1.00
267_Y	270_A	1.092	1.00
70_D	77_R	1.091	1.00
281_Q	284_K	1.089	1.00
117_Y	278_A	1.085	1.00
18_M	55_L	1.084	1.00
11_V	21_A	1.077	1.00
102_G	126_T	1.075	1.00
71_V	74_E	1.063	1.00
277_Q	281_Q	1.061	1.00
57_V	61_G	1.058	1.00
6_L	68_A	1.058	1.00
169_T	228_G	1.044	1.00
127_G	135_S	1.042	1.00
250_L	253_M	1.042	1.00
35_R	38_T	1.040	1.00
4_Q	7_H	1.039	1.00
222_K	226_L	1.034	1.00
109_V	283_I	1.033	1.00
195_Q	198_Q	1.033	1.00
185_I	221_C	1.029	1.00
8_M	25_L	1.020	1.00
63_K	67_F	1.015	1.00
108_K	227_H	1.011	1.00
223_Q	227_H	1.008	1.00
76_E	80_E	1.007	1.00
167_V	239_L	0.997	1.00
114_V	183_P	0.993	1.00
27_V	32_L	0.993	1.00
116_K	285_D	0.989	1.00
79_R	83_D	0.984	1.00
76_E	79_R	0.981	1.00
13_A	48_F	0.973	1.00
168_D	174_I	0.970	1.00
137_Y	154_G	0.969	1.00
163_H	259_G	0.968	1.00
179_H	249_P	0.967	1.00
157_D	280_V	0.966	1.00
241_N	245_V	0.965	1.00
9_L	57_V	0.961	1.00
135_S	138_E	0.958	1.00
113_Y	117_Y	0.956	1.00
183_P	210_K	0.953	1.00
64_I	68_A	0.949	1.00
109_V	282_V	0.947	1.00
166_L	231_Y	0.944	1.00
12_L	18_M	0.943	1.00
13_A	61_G	0.942	1.00
73_L	77_R	0.938	1.00
45_T	82_I	0.935	1.00
137_Y	152_W	0.934	1.00
215_V	224_M	0.933	1.00
48_F	55_L	0.932	1.00
125_I	135_S	0.926	1.00
273_L	276_V	0.923	1.00
9_L	39_I	0.920	1.00
96_A	146_I	0.917	1.00
282_V	285_D	0.916	1.00
21_A	32_L	0.907	1.00
131_E	134_K	0.903	1.00
141_V	144_G	0.901	1.00
38_T	41_K	0.895	1.00
173_C	183_P	0.884	1.00
66_Q	69_N	0.876	1.00
121_K	210_K	0.874	1.00
195_Q	199_H	0.871	1.00
20_K	24_R	0.871	1.00
239_L	242_E	0.868	1.00
19_R	23_E	0.865	1.00
120_A	275_Q	0.862	1.00
155_R	158_Y	0.860	1.00
96_A	132_M	0.859	1.00
148_G	261_D	0.855	1.00
281_Q	285_D	0.855	1.00
167_V	232_A	0.851	1.00
95_L	143_I	0.851	1.00
16_L	56_T	0.848	1.00
51_S	54_G	0.848	1.00
242_E	245_V	0.848	1.00
99_S	217_Q	0.844	1.00
12_L	36_L	0.841	1.00
186_Q	211_Q	0.840	1.00
25_L	32_L	0.836	1.00
175_E	249_P	0.832	1.00
125_I	141_V	0.828	1.00
70_D	73_L	0.821	1.00
96_A	144_G	0.818	1.00
173_C	177_I	0.816	1.00
9_L	64_I	0.810	1.00
89_I	117_Y	0.808	1.00
60_A	82_I	0.806	1.00
16_L	62_E	0.803	1.00
37_Q	46_K	0.802	1.00
91_G	275_Q	0.796	1.00
13_A	16_L	0.795	1.00
12_L	48_F	0.793	1.00
169_T	229_I	0.793	1.00
29_Q	33_S	0.792	1.00
111_K	229_I	0.787	1.00
74_E	78_I	0.782	1.00
197_I	201_W	0.778	1.00
194_F	214_L	0.777	1.00
133_L	137_Y	0.771	1.00
14_E	65_I	0.770	1.00
154_G	268_E	0.768	1.00
168_D	249_P	0.767	1.00
75_Q	78_I	0.767	1.00
91_G	120_A	0.765	1.00
143_I	279_F	0.764	1.00
224_M	229_I	0.761	1.00
167_V	234_L	0.756	1.00
63_K	85_L	0.754	1.00
184_F	209_P	0.754	1.00
60_A	85_L	0.754	1.00
171_I	175_E	0.753	1.00
163_H	252_D	0.753	1.00
145_I	283_I	0.753	1.00
3_L	72_T	0.753	1.00
15_E	21_A	0.752	1.00
83_D	86_E	0.752	1.00
57_V	62_E	0.751	1.00
274_K	278_A	0.751	1.00
183_P	211_Q	0.751	1.00
116_K	278_A	0.749	1.00
174_I	177_I	0.746	1.00
4_Q	35_R	0.743	1.00
31_A	35_R	0.743	1.00
163_H	257_P	0.741	1.00
77_R	81_N	0.739	1.00
56_T	62_E	0.736	1.00
16_L	54_G	0.736	1.00
199_H	203_Q	0.735	1.00
235_P	238_T	0.730	1.00
60_A	63_K	0.729	1.00
114_V	229_I	0.728	1.00
5_E	8_M	0.728	1.00
94_K	141_V	0.727	1.00
12_L	32_L	0.726	1.00
194_F	200_W	0.725	1.00
198_Q	202_H	0.723	1.00
68_A	71_V	0.722	1.00
78_I	82_I	0.720	1.00
174_I	182_R	0.719	1.00
127_G	132_M	0.718	1.00
113_Y	278_A	0.718	1.00
75_Q	79_R	0.718	1.00
49_L	58_T	0.713	1.00
49_L	54_G	0.711	1.00
7_H	11_V	0.705	1.00
18_M	54_G	0.704	1.00
18_M	32_L	0.701	1.00
196_E	200_W	0.700	1.00
270_A	273_L	0.697	1.00
40_E	45_T	0.695	1.00
173_C	178_A	0.693	1.00
97_V	106_L	0.693	1.00
97_V	102_G	0.692	1.00
112_T	285_D	0.690	1.00
142_H	276_V	0.689	1.00
217_Q	220_T	0.689	1.00
60_A	64_I	0.683	1.00
200_W	203_Q	0.680	1.00
213_I	224_M	0.678	1.00
272_E	277_Q	0.677	1.00
93_L	275_Q	0.677	1.00
68_A	72_T	0.677	1.00
168_D	175_E	0.675	1.00
73_L	76_E	0.671	1.00
94_K	142_H	0.667	1.00
180_T	207_T	0.667	1.00
40_E	50_R	0.666	1.00
196_E	199_H	0.666	1.00
170_E	246_N	0.665	1.00
204_K	207_T	0.664	1.00
69_N	73_L	0.659	1.00
136_L	265_L	0.659	1.00
12_L	17_N	0.659	1.00
62_E	65_I	0.655	1.00
59_P	63_K	0.655	1.00
200_W	204_K	0.653	1.00
21_A	25_L	0.651	1.00
77_R	80_E	0.651	1.00
121_K	214_L	0.650	1.00
241_N	244_K	0.650	1.00
23_E	26_F	0.648	1.00
177_I	183_P	0.643	1.00
160_M	262_T	0.643	1.00
64_I	82_I	0.643	1.00
278_A	282_V	0.643	1.00
174_I	179_H	0.640	1.00
199_H	202_H	0.640	1.00
181_E	210_K	0.639	1.00
139_D	267_Y	0.639	1.00
36_L	40_E	0.637	1.00
168_D	173_C	0.636	1.00
171_I	249_P	0.632	1.00
197_I	200_W	0.632	1.00
63_K	82_I	0.630	1.00
90_H	121_K	0.629	1.00
179_H	254_K	0.624	1.00
201_W	209_P	0.622	1.00
126_T	216_D	0.620	1.00
126_T	217_Q	0.618	1.00
224_M	230_G	0.618	1.00
279_F	283_I	0.616	1.00
171_I	228_G	0.614	1.00
7_H	10_V	0.613	1.00
103_Q	223_Q	0.612	1.00
67_F	71_V	0.612	1.00
155_R	269_P	0.609	1.00
4_Q	38_T	0.609	1.00
93_L	143_I	0.607	1.00
131_E	135_S	0.607	1.00
80_E	84_E	0.604	1.00
221_C	225_A	0.601	1.00
57_V	65_I	0.601	1.00
143_I	280_V	0.601	1.00
166_L	233_I	0.599	1.00
195_Q	200_W	0.598	1.00
106_L	109_V	0.596	1.00
28_S	34_Q	0.592	1.00
188_K	214_L	0.585	1.00
31_A	34_Q	0.585	1.00
193_Y	197_I	0.584	1.00
30_P	34_Q	0.584	1.00
274_K	277_Q	0.582	1.00
45_T	49_L	0.577	1.00
4_Q	8_M	0.577	1.00
110_L	122_I	0.574	1.00
43_W	82_I	0.574	1.00
187_F	221_C	0.571	1.00
36_L	48_F	0.569	1.00
215_V	220_T	0.568	1.00
189_S	214_L	0.567	1.00
48_F	57_V	0.566	1.00
101_I	105_W	0.564	1.00
164_L	233_I	0.563	1.00
162_D	260_R	0.562	1.00
43_W	64_I	0.559	1.00
108_K	111_K	0.559	1.00
147_R	260_R	0.558	1.00
8_M	36_L	0.557	1.00
184_F	187_F	0.556	1.00
198_Q	201_W	0.556	1.00
72_T	75_Q	0.556	1.00
193_Y	196_E	0.555	1.00
174_I	178_A	0.555	1.00
66_Q	81_N	0.553	1.00
91_G	117_Y	0.553	1.00
173_C	176_D	0.551	1.00
68_A	75_Q	0.550	1.00
234_L	239_L	0.550	1.00
91_G	119_N	0.550	1.00
108_K	112_T	0.545	1.00
266_G	277_Q	0.543	1.00
43_W	46_K	0.543	1.00
7_H	72_T	0.541	1.00
67_F	82_I	0.539	1.00
72_T	76_E	0.538	1.00
176_D	179_H	0.537	1.00
103_Q	217_Q	0.536	1.00
18_M	29_Q	0.535	1.00
166_L	184_F	0.534	1.00
18_M	50_R	0.534	1.00
96_A	127_G	0.534	1.00
96_A	125_I	0.534	1.00
218_I	235_P	0.533	1.00
6_L	64_I	0.530	1.00
145_I	264_L	0.530	1.00
46_K	60_A	0.528	1.00
8_M	21_A	0.525	1.00
27_V	35_R	0.520	1.00
192_T	195_Q	0.519	1.00
117_Y	120_A	0.519	1.00
71_V	79_R	0.519	1.00
184_F	231_Y	0.517	1.00
16_L	55_L	0.515	1.00
150_P	153_K	0.512	1.00
148_G	156_K	0.509	1.00
148_G	152_W	0.509	1.00
276_V	280_V	0.508	1.00
105_W	109_V	0.506	1.00
97_V	124_L	0.505	1.00
16_L	57_V	0.502	1.00
159_L	264_L	0.501	1.00
242_E	246_N	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
3fxqA	3	0.9795	100	0.099	Contact Map
2esnA	3	0.9795	100	0.099	Contact Map
1ixcA	4	0.9727	100	0.11	Contact Map
1al3A	1	0.7031	100	0.11	Contact Map
1uthA	2	0.7543	100	0.112	Contact Map
2h98A	2	0.6826	100	0.113	Contact Map
3fzvA	4	0.9556	100	0.114	Contact Map
2h9bA	2	0.6826	100	0.116	Contact Map
4x6gA	4	0.9966	100	0.118	Contact Map
3szpA	3	0.9659	100	0.131	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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