YAHB - ECOLI - GREMLIN Contacts

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

YAHB - Uncharacterized HTH-type transcriptional regulator YahB

UniProt:	P77700	Sequences: MNSIFTEENLLAFTTAARFGSFSKAAEELGLTTSAISYTIKRMETGLDVVLFTRSTRSIELTESGRYFFRKATDLLNDFYAIKRRIDTISQGIEARVRICINQLLYTPKHTARLLQVLKKQFPTCQITVTTEVYNGVWDAIINNQANIAIGAPDTLLDGGGIDYTEIGAIRWAFAIAPDHPLAFVPEPIAESQLRLYPNIMVEDTAHTINKKVGWLLHGQESILVPDFNTKCQCQILGEGIGFLPDYMVREAMTQSLLVTRQIHNPRQDSRMLLATQHSATGQVTQWIKKQFAPNGILTGIYQDLLHREN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13586
Length:	310 (283)
Sequences:	79760 (57930)
Seq/√Len:	3443.6

ECOLI - YAHB YDHB YEEY DMLR OXYR ALLS TTDR CYSB ABGR YBHD YHAJ CYNR LYSR TDCA YIAU CBL LEUO NAC ILVY AAER YFER YDCI YAFC YCAN YNEJ HCAR PGRR GCVA DSDC YHJC XAPR YNFL YBDO METR YFIE YEIE YBEF NHAR YIDZ YGFI LRHA ICIA PERR YJIE HDFR
BACSU - CYSL YWBI YCGK ALSR YVBU BSDA GLTC GLTR YTLI YYBE CITR YWQM YXJO YUST YOFA YKUM CZCR YRAN 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
74_D	78_D	3.485	1.00
19_F	28_E	3.311	1.00
165_T	293_A	2.613	1.00
100_C	146_A	2.495	1.00
71_K	85_R	2.371	1.00
235_Q	242_G	2.252	1.00
180_H	197_Y	2.231	1.00
171_R	246_D	2.172	1.00
169_A	271_R	2.172	1.00
15_T	28_E	2.158	1.00
117_V	295_N	2.157	1.00
166_E	169_A	2.116	1.00
96_R	128_T	2.112	1.00
18_R	73_T	2.075	1.00
24_K	27_E	2.073	1.00
96_R	126_Q	2.063	1.00
166_E	271_R	2.039	1.00
190_A	193_Q	2.012	1.00
49_V	64_S	1.988	1.00
12_A	39_T	1.986	1.00
169_A	269_D	1.957	1.00
14_T	69_F	1.953	1.00
232_C	252_A	1.951	1.00
98_R	128_T	1.944	1.00
236_I	257_L	1.929	1.00
71_K	78_D	1.916	1.00
117_V	291_Q	1.903	1.00
14_T	73_T	1.894	1.00
15_T	18_R	1.880	1.00
176_I	261_R	1.874	1.00
75_L	79_F	1.850	1.00
12_A	36_I	1.849	1.00
15_T	19_F	1.843	1.00
17_A	61_L	1.835	1.00
14_T	18_R	1.829	1.00
200_I	240_G	1.824	1.00
22_F	40_I	1.810	1.00
173_A	246_D	1.788	1.00
69_F	73_T	1.783	1.00
137_V	149_A	1.743	1.00
53_T	60_E	1.704	1.00
68_F	82_I	1.703	1.00
236_I	252_A	1.668	1.00
198_P	222_S	1.646	1.00
67_Y	85_R	1.640	1.00
173_A	260_T	1.635	1.00
164_Y	273_L	1.629	1.00
140_A	145_Q	1.625	1.00
118_L	288_I	1.616	1.00
18_R	28_E	1.588	1.00
17_A	69_F	1.559	1.00
13_F	69_F	1.556	1.00
14_T	72_A	1.551	1.00
19_F	24_K	1.544	1.00
12_A	31_L	1.529	1.00
163_D	278_H	1.522	1.00
118_L	125_C	1.501	1.00
23_S	33_T	1.491	1.00
9_N	39_T	1.487	1.00
92_G	124_T	1.486	1.00
185_V	193_Q	1.485	1.00
139_D	143_N	1.477	1.00
63_E	66_R	1.474	1.00
9_N	46_G	1.442	1.00
165_T	276_T	1.438	1.00
281_T	285_T	1.429	1.00
50_V	53_T	1.427	1.00
32_T	35_A	1.422	1.00
21_S	24_K	1.413	1.00
9_N	42_R	1.410	1.00
14_T	76_L	1.406	1.00
153_P	273_L	1.405	1.00
71_K	74_D	1.403	1.00
6_T	9_N	1.401	1.00
289_K	293_A	1.391	1.00
15_T	29_L	1.385	1.00
163_D	276_T	1.382	1.00
151_G	275_A	1.381	1.00
71_K	81_A	1.368	1.00
75_L	82_I	1.364	1.00
178_P	257_L	1.347	1.00
276_T	289_K	1.347	1.00
94_E	124_T	1.336	1.00
274_L	289_K	1.318	1.00
117_V	121_Q	1.316	1.00
98_R	130_T	1.310	1.00
142_I	161_G	1.307	1.00
287_W	290_K	1.302	1.00
7_E	79_F	1.298	1.00
141_I	149_A	1.296	1.00
148_I	285_T	1.295	1.00
140_A	146_A	1.286	1.00
148_I	274_L	1.272	1.00
197_Y	241_I	1.268	1.00
55_S	60_E	1.267	1.00
176_I	241_I	1.267	1.00
170_I	247_Y	1.256	1.00
119_K	222_S	1.256	1.00
46_G	83_K	1.256	1.00
68_F	83_K	1.255	1.00
231_K	242_G	1.232	1.00
246_D	250_R	1.228	1.00
78_D	81_A	1.225	1.00
121_Q	291_Q	1.224	1.00
66_R	70_R	1.200	1.00
180_H	183_A	1.199	1.00
70_R	74_D	1.198	1.00
41_K	45_T	1.198	1.00
233_Q	236_I	1.185	1.00
178_P	259_V	1.182	1.00
67_Y	70_R	1.178	1.00
71_K	82_I	1.171	1.00
13_F	52_F	1.171	1.00
246_D	260_T	1.169	1.00
250_R	254_T	1.165	1.00
117_V	120_K	1.162	1.00
119_K	198_P	1.159	1.00
116_Q	120_K	1.155	1.00
164_Y	275_A	1.150	1.00
166_E	273_L	1.149	1.00
176_I	180_H	1.140	1.00
252_A	257_L	1.139	1.00
13_F	51_L	1.133	1.00
31_L	35_A	1.127	1.00
200_I	231_K	1.126	1.00
97_V	288_I	1.120	1.00
13_F	17_A	1.119	1.00
212_K	217_L	1.110	1.00
38_Y	41_K	1.110	1.00
38_Y	42_R	1.096	1.00
11_L	80_Y	1.095	1.00
128_T	224_L	1.094	1.00
277_Q	280_A	1.094	1.00
37_S	41_K	1.094	1.00
225_V	231_K	1.087	1.00
175_A	260_T	1.086	1.00
122_F	287_W	1.086	1.00
74_D	81_A	1.085	1.00
118_L	291_Q	1.082	1.00
16_A	25_A	1.081	1.00
290_K	293_A	1.080	1.00
116_Q	237_L	1.078	1.00
198_P	220_Q	1.077	1.00
22_F	59_I	1.077	1.00
8_E	11_L	1.074	1.00
10_L	72_A	1.058	1.00
188_P	264_H	1.058	1.00
15_T	25_A	1.056	1.00
75_L	78_D	1.052	1.00
39_T	42_R	1.046	1.00
286_Q	290_K	1.045	1.00
291_Q	295_N	1.037	1.00
114_L	292_F	1.031	1.00
142_I	159_G	1.030	1.00
177_A	238_G	1.028	1.00
67_Y	71_K	1.027	1.00
232_C	236_I	1.020	1.00
61_L	65_G	1.019	1.00
233_Q	237_L	1.010	1.00
260_T	263_I	1.010	1.00
113_R	237_L	1.008	1.00
189_I	193_Q	1.008	1.00
165_T	289_K	1.008	1.00
83_K	87_D	0.980	1.00
174_F	241_I	0.979	1.00
31_L	36_I	0.979	1.00
12_A	29_L	0.979	1.00
80_Y	83_K	0.975	1.00
100_C	137_V	0.975	1.00
80_Y	84_R	0.975	1.00
171_R	269_D	0.974	1.00
175_A	249_V	0.970	1.00
191_E	265_N	0.968	1.00
17_A	52_F	0.963	1.00
121_Q	294_P	0.957	1.00
251_E	255_Q	0.952	1.00
176_I	182_L	0.947	1.00
16_A	22_F	0.947	1.00
118_L	122_F	0.945	1.00
77_N	81_A	0.944	1.00
13_F	61_L	0.941	1.00
130_T	140_A	0.930	1.00
291_Q	294_P	0.929	1.00
211_K	215_W	0.925	1.00
68_F	72_A	0.924	1.00
201_M	221_E	0.924	1.00
52_F	59_I	0.922	1.00
140_A	143_N	0.920	1.00
13_F	43_M	0.916	1.00
225_V	234_C	0.915	1.00
25_A	36_I	0.914	1.00
282_G	285_T	0.911	1.00
107_T	229_N	0.910	1.00
49_V	86_I	0.907	1.00
161_G	278_H	0.906	1.00
17_A	65_G	0.902	1.00
42_R	45_T	0.901	1.00
249_V	252_A	0.894	1.00
114_L	291_Q	0.894	1.00
126_Q	220_Q	0.891	1.00
180_H	198_P	0.888	1.00
146_A	149_A	0.888	1.00
70_R	73_T	0.883	1.00
24_K	28_E	0.880	1.00
193_Q	196_L	0.875	1.00
67_Y	89_I	0.874	1.00
103_Q	227_D	0.867	1.00
153_P	271_R	0.865	1.00
99_I	148_I	0.865	1.00
162_I	275_A	0.863	1.00
100_C	151_G	0.854	1.00
163_D	166_E	0.853	1.00
125_C	284_V	0.852	1.00
290_K	294_P	0.851	1.00
23_S	27_E	0.847	1.00
20_G	60_E	0.846	1.00
175_A	242_G	0.842	1.00
55_S	58_S	0.839	1.00
198_P	221_E	0.838	1.00
183_A	259_V	0.837	1.00
138_W	142_I	0.829	1.00
74_D	77_N	0.824	1.00
29_L	36_I	0.822	1.00
64_S	89_I	0.820	1.00
8_E	39_T	0.818	1.00
130_T	146_A	0.818	1.00
253_M	256_S	0.818	1.00
209_I	213_V	0.813	1.00
179_D	183_A	0.812	1.00
281_T	286_Q	0.811	1.00
100_C	149_A	0.811	1.00
13_F	68_F	0.811	1.00
41_K	50_V	0.802	1.00
64_S	86_I	0.802	1.00
249_V	253_M	0.800	1.00
177_A	239_E	0.799	1.00
16_A	40_I	0.797	1.00
208_T	212_K	0.796	1.00
20_G	66_R	0.796	1.00
7_E	76_L	0.795	1.00
93_I	122_F	0.794	1.00
95_A	284_V	0.785	1.00
17_A	20_G	0.783	1.00
33_T	37_S	0.781	1.00
116_Q	239_E	0.778	1.00
212_K	215_W	0.778	1.00
192_S	195_R	0.777	1.00
252_A	255_Q	0.777	1.00
136_G	139_D	0.777	1.00
18_R	69_F	0.776	1.00
16_A	52_F	0.775	1.00
148_I	288_I	0.771	1.00
78_D	82_I	0.771	1.00
95_A	125_C	0.764	1.00
171_R	262_Q	0.763	1.00
19_F	25_A	0.760	1.00
234_C	239_E	0.757	1.00
177_A	180_H	0.756	1.00
79_F	82_I	0.751	1.00
20_G	58_S	0.750	1.00
117_V	294_P	0.750	1.00
121_Q	287_W	0.750	1.00
81_A	85_R	0.748	1.00
9_N	12_A	0.747	1.00
190_A	264_H	0.744	1.00
79_F	83_K	0.742	1.00
208_T	211_K	0.740	1.00
283_Q	287_W	0.739	1.00
64_S	67_Y	0.736	1.00
176_I	259_V	0.734	1.00
142_I	162_I	0.732	1.00
211_K	214_G	0.730	1.00
119_K	239_E	0.728	1.00
61_L	66_R	0.728	1.00
60_E	66_R	0.726	1.00
114_L	295_N	0.725	1.00
175_A	244_L	0.724	1.00
82_I	86_I	0.723	1.00
87_D	90_S	0.722	1.00
182_L	197_Y	0.717	1.00
72_A	75_L	0.716	1.00
22_F	36_I	0.715	1.00
98_R	146_A	0.714	1.00
175_A	253_M	0.713	1.00
11_L	15_T	0.711	1.00
53_T	62_T	0.710	1.00
118_L	287_W	0.708	1.00
150_I	292_F	0.708	1.00
16_A	36_I	0.703	1.00
190_A	265_N	0.703	1.00
185_V	198_P	0.702	1.00
245_P	248_M	0.702	1.00
101_I	106_Y	0.696	1.00
253_M	260_T	0.696	1.00
35_A	39_T	0.694	1.00
195_R	217_L	0.691	1.00
196_L	220_Q	0.689	1.00
73_T	77_N	0.688	1.00
53_T	58_S	0.688	1.00
236_I	255_Q	0.684	1.00
188_P	262_Q	0.683	1.00
44_E	49_V	0.680	1.00
64_S	68_F	0.680	1.00
210_N	214_G	0.678	1.00
147_N	285_T	0.678	1.00
223_I	234_C	0.675	1.00
98_R	147_N	0.674	1.00
202_V	231_K	0.674	1.00
227_D	230_T	0.671	1.00
199_N	219_G	0.669	1.00
180_H	185_V	0.668	1.00
101_I	111_T	0.668	1.00
77_N	80_Y	0.668	1.00
287_W	291_Q	0.667	1.00
97_V	284_V	0.666	1.00
72_A	76_L	0.665	1.00
144_N	277_Q	0.663	1.00
22_F	58_S	0.663	1.00
63_E	67_Y	0.660	1.00
81_A	84_R	0.658	1.00
210_N	213_V	0.658	1.00
179_D	259_V	0.654	1.00
66_R	69_F	0.654	1.00
44_E	54_R	0.653	1.00
251_E	254_T	0.651	1.00
141_I	275_A	0.650	1.00
203_E	224_L	0.646	1.00
25_A	29_L	0.645	1.00
68_F	86_I	0.645	1.00
126_Q	224_L	0.644	1.00
27_E	30_G	0.639	1.00
199_N	241_I	0.635	1.00
8_E	42_R	0.633	1.00
40_I	44_E	0.631	1.00
179_D	238_G	0.627	1.00
16_A	21_S	0.624	1.00
71_K	75_L	0.622	1.00
174_F	194_L	0.622	1.00
97_V	148_I	0.620	1.00
67_Y	86_I	0.619	1.00
168_G	272_M	0.619	1.00
11_L	14_T	0.618	1.00
178_P	256_S	0.618	1.00
283_Q	286_Q	0.612	1.00
174_F	243_F	0.612	1.00
182_L	185_V	0.609	1.00
94_E	126_Q	0.607	1.00
288_I	292_F	0.604	1.00
106_Y	134_Y	0.601	1.00
61_L	69_F	0.601	1.00
34_S	38_Y	0.601	1.00
148_I	289_K	0.600	1.00
234_C	240_G	0.598	1.00
203_E	226_P	0.597	1.00
111_T	114_L	0.596	1.00
176_I	183_A	0.595	1.00
174_F	199_N	0.595	1.00
84_R	88_T	0.594	1.00
231_K	235_Q	0.592	1.00
171_R	266_P	0.591	1.00
163_D	279_S	0.590	1.00
170_I	270_S	0.588	1.00
152_A	270_S	0.588	1.00
47_L	86_I	0.584	1.00
276_T	286_Q	0.582	1.00
141_I	162_I	0.580	1.00
107_T	233_Q	0.576	1.00
35_A	38_Y	0.575	1.00
113_R	117_V	0.574	1.00
32_T	38_Y	0.574	1.00
188_P	193_Q	0.572	1.00
113_R	116_Q	0.571	1.00
172_W	243_F	0.571	1.00
136_G	140_A	0.569	1.00
8_E	12_A	0.566	1.00
47_L	68_F	0.565	1.00
115_L	127_I	0.565	1.00
225_V	230_T	0.565	1.00
204_D	224_L	0.564	1.00
185_V	188_P	0.563	1.00
49_V	53_T	0.562	1.00
105_L	110_H	0.560	1.00
11_L	76_L	0.559	1.00
52_F	61_L	0.556	1.00
76_L	79_F	0.552	1.00
47_L	50_V	0.550	1.00
180_H	241_I	0.547	1.00
95_A	124_T	0.546	1.00
40_I	52_F	0.541	1.00
70_R	85_R	0.541	1.00
167_I	274_L	0.540	1.00
12_A	40_I	0.540	1.00
244_L	249_V	0.540	1.00
95_A	122_F	0.536	1.00
76_L	80_Y	0.536	1.00
100_C	130_T	0.534	1.00
228_F	245_P	0.533	1.00
153_P	164_Y	0.532	1.00
139_D	145_Q	0.531	1.00
150_I	274_L	0.531	1.00
137_V	144_N	0.529	1.00
13_F	65_G	0.529	1.00
22_F	33_T	0.529	1.00
72_A	79_F	0.528	1.00
122_F	125_C	0.527	1.00
285_T	289_K	0.526	1.00
192_S	215_W	0.524	1.00
157_L	160_G	0.524	1.00
88_T	93_I	0.521	1.00
22_F	54_R	0.520	1.00
276_T	281_T	0.514	1.00
50_V	64_S	0.513	1.00
71_K	86_I	0.513	1.00
12_A	25_A	0.512	1.00
263_I	266_P	0.511	1.00
31_L	39_T	0.508	1.00
113_R	233_Q	0.508	1.00
75_L	83_K	0.507	1.00
84_R	87_D	0.505	1.00
20_G	59_I	0.504	1.00
10_L	68_F	0.504	1.00
109_K	112_A	0.502	1.00
17_A	66_R	0.502	1.00
101_I	129_V	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	0.9419	100	0.134	Contact Map
1uthA	2	0.7161	100	0.134	Contact Map
3fzvA	4	0.9194	100	0.136	Contact Map
1ixcA	4	0.929	100	0.139	Contact Map
2h98A	2	0.671	100	0.144	Contact Map
3fxqA	3	0.9355	100	0.144	Contact Map
4x6gA	4	0.9677	100	0.145	Contact Map
1al3A	1	0.7	100	0.146	Contact Map
2h9bA	2	0.6742	100	0.146	Contact Map
3szpA	3	0.9194	100	0.165	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 0.0115 seconds.