YAFC - ECOLI - GREMLIN Contacts

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YAFC - Uncharacterized HTH-type transcriptional regulator YafC

UniProt:	P30864	Sequences: MKATSEELAIFVSVVESGSFSRAAEQLGQANSAVSRAVKKLEMKLGVSLLNRTTRQLSLTEEGERYFRRVQSILQEMAAAESEIMETRNTPRGLLRIDAATPVVLHFLMPLIKPFRERYPEVTLSLVSSETIINLIERKVDVAIRAGTLTDSSLRARPLFNSYRKIIASPDYISRYGKPETIDDLKQHICLGFTEPASLNTWPIARSDGQLHEVKYGLSSNSGETLKQLCLSGNGIACLSDYMIDKEIARGELVELMADKVLPVEMPFSAVYYSDRAVSTRIRAFIDFLSEHVKTAPGGAVREA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11649
Length:	304 (286)
Sequences:	79947 (58052)
Seq/√Len:	3432.7

ECOLI - YAFC YCAN YFER YBHD OXYR LYSR TTDR PGRR AAER YEEY DMLR YEIE CYNR YNFL CYSB CBL NAC GCVA DSDC LEUO YHJC ABGR TDCA YAHB YDCI YBDO METR YBEF YIDZ NHAR YDHB HCAR ILVY XAPR ALLS YFIE YNEJ ICIA YIAU YHAJ YGFI LRHA YJIE PERR HDFR
BACSU - CYSL YCGK YWBI YTLI GLTR ALSR GLTC CITR YYBE BSDA YWQM YVBU YUST YOFA YOAU YKUM YXJO 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
72_S	76_E	3.601	1.00
17_S	26_Q	3.390	1.00
157_R	290_S	2.675	1.00
98_D	140_V	2.601	1.00
69_R	83_E	2.431	1.00
13_S	26_Q	2.294	1.00
230_C	237_A	2.293	1.00
114_P	292_H	2.208	1.00
172_Y	188_H	2.205	1.00
158_P	161_N	2.189	1.00
161_N	267_P	2.188	1.00
94_L	125_S	2.162	1.00
163_Y	241_D	2.162	1.00
158_P	267_P	2.116	1.00
22_R	25_E	2.074	1.00
47_V	62_E	2.064	1.00
94_L	123_T	2.054	1.00
10_I	37_A	2.047	1.00
16_E	71_Q	2.045	1.00
181_T	184_D	2.023	1.00
161_N	265_E	1.995	1.00
227_K	247_E	1.986	1.00
69_R	76_E	1.976	1.00
12_V	71_Q	1.971	1.00
114_P	288_F	1.961	1.00
12_V	67_F	1.958	1.00
231_L	252_E	1.932	1.00
12_V	16_E	1.929	1.00
13_S	16_E	1.921	1.00
96_R	125_S	1.904	1.00
191_L	235_G	1.900	1.00
10_I	34_V	1.895	1.00
13_S	17_S	1.894	1.00
165_K	241_D	1.889	1.00
15_V	59_L	1.873	1.00
73_I	77_M	1.867	1.00
231_L	247_E	1.851	1.00
168_A	256_L	1.820	1.00
67_F	71_Q	1.802	1.00
20_F	38_V	1.769	1.00
51_N	58_S	1.716	1.00
66_Y	80_A	1.709	1.00
189_I	217_G	1.693	1.00
165_K	255_E	1.693	1.00
156_A	269_S	1.680	1.00
65_R	83_E	1.672	1.00
177_G	184_D	1.622	1.00
15_V	67_F	1.611	1.00
115_F	285_F	1.585	1.00
134_N	139_K	1.580	1.00
17_S	22_R	1.577	1.00
16_E	26_Q	1.567	1.00
12_V	70_V	1.563	1.00
11_F	67_F	1.546	1.00
155_R	274_S	1.540	1.00
10_I	29_Q	1.515	1.00
7_E	37_A	1.508	1.00
133_I	137_E	1.499	1.00
90_T	121_E	1.499	1.00
21_S	31_N	1.485	1.00
157_R	272_Y	1.473	1.00
7_E	44_K	1.471	1.00
19_S	22_R	1.465	1.00
69_R	72_S	1.465	1.00
30_A	33_A	1.449	1.00
7_E	40_K	1.448	1.00
48_S	51_N	1.445	1.00
61_E	64_E	1.436	1.00
115_F	122_V	1.427	1.00
13_S	27_L	1.424	1.00
147_G	269_S	1.417	1.00
286_I	290_S	1.410	1.00
278_V	282_I	1.401	1.00
12_V	74_L	1.401	1.00
145_R	271_V	1.399	1.00
155_R	272_Y	1.396	1.00
69_R	79_A	1.379	1.00
4_T	7_E	1.378	1.00
200_N	204_I	1.366	1.00
73_I	80_A	1.365	1.00
105_L	224_E	1.359	1.00
92_R	121_E	1.346	1.00
272_Y	286_I	1.345	1.00
134_N	140_V	1.337	1.00
5_S	77_M	1.324	1.00
284_A	287_D	1.319	1.00
53_T	58_S	1.317	1.00
135_L	143_A	1.314	1.00
162_S	242_Y	1.312	1.00
136_I	153_S	1.311	1.00
114_P	118_R	1.304	1.00
170_P	252_E	1.301	1.00
270_A	286_I	1.295	1.00
66_Y	81_E	1.282	1.00
76_E	79_A	1.282	1.00
142_V	282_I	1.281	1.00
142_V	270_A	1.280	1.00
168_A	236_I	1.273	1.00
116_R	217_G	1.267	1.00
118_R	288_F	1.265	1.00
226_L	237_A	1.257	1.00
247_E	252_E	1.249	1.00
44_K	81_E	1.244	1.00
188_H	236_I	1.244	1.00
68_R	72_S	1.234	1.00
228_Q	231_L	1.217	1.00
69_R	80_A	1.208	1.00
241_D	245_D	1.202	1.00
116_R	189_I	1.197	1.00
241_D	255_E	1.192	1.00
65_R	68_R	1.191	1.00
245_D	249_A	1.186	1.00
113_K	117_E	1.185	1.00
11_F	50_L	1.185	1.00
158_P	269_S	1.184	1.00
29_Q	33_A	1.183	1.00
64_E	68_R	1.172	1.00
39_K	43_M	1.168	1.00
178_K	254_V	1.165	1.00
170_P	254_V	1.161	1.00
128_S	131_T	1.151	1.00
11_F	15_V	1.147	1.00
207_S	212_H	1.146	1.00
173_I	188_H	1.140	1.00
156_A	271_V	1.139	1.00
36_R	40_K	1.136	1.00
11_F	49_L	1.124	1.00
113_K	232_S	1.121	1.00
114_P	117_E	1.119	1.00
36_R	39_K	1.118	1.00
191_L	226_L	1.108	1.00
179_P	259_D	1.096	1.00
189_I	215_K	1.094	1.00
72_S	79_A	1.085	1.00
20_F	57_L	1.083	1.00
95_L	285_F	1.082	1.00
287_D	290_S	1.081	1.00
35_S	39_K	1.078	1.00
8_L	70_V	1.071	1.00
14_V	23_A	1.069	1.00
227_K	231_L	1.067	1.00
255_E	258_A	1.067	1.00
6_E	9_A	1.066	1.00
119_Y	284_A	1.066	1.00
125_S	219_S	1.065	1.00
115_F	288_F	1.062	1.00
65_R	69_R	1.062	1.00
13_S	23_A	1.056	1.00
73_I	76_E	1.051	1.00
288_F	292_H	1.048	1.00
37_A	40_K	1.046	1.00
111_L	289_L	1.043	1.00
283_R	287_D	1.041	1.00
110_P	232_S	1.039	1.00
220_S	226_L	1.038	1.00
157_R	286_I	1.036	1.00
167_I	255_E	1.035	1.00
9_A	78_A	1.033	1.00
180_E	184_D	1.030	1.00
136_I	151_D	1.021	1.00
169_S	233_G	1.021	1.00
228_Q	232_S	1.017	1.00
59_L	63_G	1.017	1.00
201_T	204_I	1.003	1.00
81_E	85_M	1.000	1.00
182_I	260_K	0.991	1.00
163_Y	265_E	0.990	1.00
167_I	244_I	0.987	1.00
246_K	250_R	0.987	1.00
166_I	236_I	0.976	1.00
29_Q	34_V	0.973	1.00
127_V	130_E	0.969	1.00
10_I	27_L	0.966	1.00
78_A	82_S	0.966	1.00
115_F	119_Y	0.965	1.00
75_Q	79_A	0.965	1.00
14_V	20_F	0.961	1.00
78_A	81_E	0.960	1.00
15_V	50_L	0.957	1.00
168_A	172_Y	0.954	1.00
66_Y	70_V	0.952	1.00
134_N	137_E	0.939	1.00
11_F	59_L	0.938	1.00
192_G	216_Y	0.938	1.00
288_F	291_E	0.932	1.00
118_R	291_E	0.931	1.00
220_S	229_L	0.928	1.00
279_S	282_I	0.926	1.00
172_Y	175_R	0.922	1.00
40_K	43_M	0.921	1.00
23_A	34_V	0.916	1.00
11_F	41_L	0.905	1.00
50_L	57_L	0.901	1.00
98_D	145_R	0.900	1.00
111_L	288_F	0.895	1.00
22_R	26_Q	0.889	1.00
47_V	84_I	0.888	1.00
140_V	143_A	0.888	1.00
65_R	87_T	0.882	1.00
98_D	143_A	0.879	1.00
190_C	214_V	0.878	1.00
101_T	222_S	0.878	1.00
15_V	63_G	0.877	1.00
123_T	215_K	0.876	1.00
147_G	267_P	0.871	1.00
273_Y	276_R	0.865	1.00
127_V	131_T	0.863	1.00
68_R	71_Q	0.860	1.00
18_G	58_S	0.857	1.00
72_S	75_Q	0.851	1.00
206_R	210_Q	0.850	1.00
53_T	56_Q	0.849	1.00
172_Y	189_I	0.845	1.00
21_S	25_E	0.841	1.00
6_E	37_A	0.841	1.00
97_I	142_V	0.840	1.00
154_L	271_V	0.838	1.00
173_I	178_K	0.835	1.00
184_D	187_Q	0.831	1.00
203_P	207_S	0.829	1.00
27_L	34_V	0.827	1.00
62_E	87_T	0.827	1.00
172_Y	176_Y	0.824	1.00
167_I	237_A	0.824	1.00
122_V	281_R	0.824	1.00
153_S	274_S	0.823	1.00
287_D	291_E	0.821	1.00
247_E	250_R	0.820	1.00
155_R	158_P	0.819	1.00
168_A	173_I	0.819	1.00
189_I	216_Y	0.813	1.00
278_V	283_R	0.812	1.00
132_I	136_I	0.811	1.00
174_S	188_H	0.806	1.00
93_G	281_R	0.804	1.00
5_S	74_L	0.803	1.00
62_E	84_I	0.800	1.00
176_Y	189_I	0.800	1.00
15_V	18_G	0.798	1.00
11_F	66_Y	0.792	1.00
113_K	234_N	0.792	1.00
18_G	64_E	0.789	1.00
77_M	80_A	0.787	1.00
244_I	247_E	0.786	1.00
39_K	48_S	0.785	1.00
31_N	35_S	0.780	1.00
181_T	259_D	0.778	1.00
14_V	38_V	0.774	1.00
14_V	50_L	0.773	1.00
183_D	186_K	0.773	1.00
79_A	83_E	0.771	1.00
201_T	205_A	0.771	1.00
77_M	81_E	0.770	1.00
16_E	67_F	0.770	1.00
116_R	234_N	0.769	1.00
18_G	56_Q	0.763	1.00
62_E	65_R	0.762	1.00
17_S	23_A	0.760	1.00
169_S	234_N	0.758	1.00
76_E	80_A	0.758	1.00
229_L	234_N	0.747	1.00
203_P	206_R	0.746	1.00
91_P	119_Y	0.745	1.00
111_L	292_H	0.745	1.00
167_I	239_L	0.744	1.00
142_V	285_F	0.744	1.00
7_E	10_I	0.744	1.00
280_T	284_A	0.744	1.00
96_R	140_V	0.742	1.00
118_R	284_A	0.742	1.00
171_D	175_R	0.734	1.00
99_A	104_V	0.730	1.00
85_M	88_R	0.729	1.00
9_A	13_S	0.728	1.00
20_F	34_V	0.722	1.00
70_V	73_I	0.720	1.00
14_V	34_V	0.719	1.00
114_P	291_E	0.718	1.00
136_I	154_L	0.717	1.00
115_F	284_A	0.716	1.00
80_A	84_I	0.716	1.00
59_L	64_E	0.714	1.00
163_Y	257_M	0.712	1.00
51_N	60_T	0.712	1.00
186_K	212_H	0.707	1.00
240_S	243_M	0.702	1.00
58_S	64_E	0.700	1.00
169_S	172_Y	0.699	1.00
71_Q	75_Q	0.699	1.00
222_S	225_T	0.691	1.00
200_N	219_S	0.690	1.00
206_R	209_G	0.689	1.00
33_A	37_A	0.685	1.00
51_N	56_Q	0.685	1.00
168_A	174_S	0.682	1.00
141_D	282_I	0.682	1.00
175_R	254_V	0.681	1.00
62_E	66_Y	0.680	1.00
96_R	141_D	0.680	1.00
168_A	254_V	0.680	1.00
64_E	67_F	0.680	1.00
181_T	260_K	0.678	1.00
202_W	206_R	0.675	1.00
183_D	210_Q	0.670	1.00
42_E	47_V	0.668	1.00
93_G	122_V	0.668	1.00
194_T	219_S	0.667	1.00
20_F	56_Q	0.665	1.00
61_E	65_R	0.663	1.00
179_P	257_M	0.661	1.00
187_Q	215_K	0.660	1.00
193_F	226_L	0.660	1.00
123_T	219_S	0.659	1.00
205_A	209_G	0.655	1.00
79_A	82_S	0.652	1.00
218_L	229_L	0.652	1.00
284_A	288_F	0.651	1.00
42_E	52_R	0.651	1.00
171_D	233_G	0.651	1.00
75_Q	78_A	0.649	1.00
138_R	273_Y	0.649	1.00
66_Y	84_I	0.647	1.00
190_C	236_I	0.644	1.00
199_L	203_P	0.643	1.00
205_A	208_D	0.643	1.00
204_I	207_S	0.642	1.00
95_L	281_R	0.642	1.00
9_A	12_V	0.642	1.00
6_E	40_K	0.639	1.00
246_K	249_A	0.636	1.00
99_A	108_L	0.635	1.00
171_D	174_S	0.634	1.00
25_E	28_G	0.633	1.00
69_R	73_I	0.632	1.00
105_L	228_Q	0.631	1.00
38_V	42_E	0.627	1.00
144_I	289_L	0.627	1.00
70_V	74_L	0.625	1.00
104_V	128_S	0.620	1.00
14_V	19_S	0.618	1.00
23_A	27_L	0.617	1.00
163_Y	263_P	0.617	1.00
204_I	208_D	0.615	1.00
96_R	127_V	0.610	1.00
276_R	279_S	0.610	1.00
142_V	286_I	0.609	1.00
166_I	185_L	0.603	1.00
170_P	251_G	0.602	1.00
171_D	254_V	0.602	1.00
166_I	238_C	0.601	1.00
280_T	283_R	0.600	1.00
201_T	206_R	0.594	1.00
82_S	86_E	0.588	1.00
162_S	266_M	0.587	1.00
108_L	111_L	0.586	1.00
135_L	271_V	0.586	1.00
226_L	230_C	0.586	1.00
65_R	84_I	0.586	1.00
194_T	221_N	0.585	1.00
95_L	142_V	0.584	1.00
177_G	180_E	0.583	1.00
272_Y	283_R	0.582	1.00
146_A	266_M	0.581	1.00
174_S	177_G	0.581	1.00
110_P	113_K	0.581	1.00
285_F	289_L	0.581	1.00
110_P	114_P	0.581	1.00
173_I	176_Y	0.580	1.00
30_A	36_R	0.574	1.00
9_A	74_L	0.574	1.00
45_L	66_Y	0.573	1.00
166_I	190_C	0.571	1.00
33_A	36_R	0.568	1.00
6_E	10_I	0.568	1.00
220_S	225_T	0.568	1.00
135_L	154_L	0.566	1.00
59_L	67_F	0.565	1.00
207_S	214_V	0.565	1.00
45_L	84_I	0.565	1.00
47_V	51_N	0.564	1.00
160_F	268_F	0.564	1.00
164_R	238_C	0.564	1.00
229_L	235_G	0.562	1.00
32_S	36_R	0.561	1.00
92_R	123_T	0.560	1.00
199_L	202_W	0.558	1.00
50_L	59_L	0.556	1.00
252_E	255_E	0.555	1.00
195_E	219_S	0.554	1.00
155_R	275_D	0.549	1.00
74_L	78_A	0.548	1.00
172_Y	236_I	0.544	1.00
11_F	63_G	0.542	1.00
174_S	180_E	0.538	1.00
239_L	244_I	0.538	1.00
45_L	48_S	0.537	1.00
186_K	213_E	0.536	1.00
173_I	177_G	0.536	1.00
10_I	38_V	0.535	1.00
133_I	139_K	0.530	1.00
147_G	156_A	0.529	1.00
68_R	83_E	0.527	1.00
223_G	240_S	0.525	1.00
10_I	23_A	0.524	1.00
159_L	270_A	0.524	1.00
20_F	31_N	0.522	1.00
48_S	62_E	0.521	1.00
103_V	107_F	0.520	1.00
282_I	286_I	0.519	1.00
20_F	52_R	0.515	1.00
144_I	270_A	0.515	1.00
105_L	222_S	0.514	1.00
38_V	50_L	0.514	1.00
247_E	251_G	0.513	1.00
168_A	175_R	0.513	1.00
112_I	124_L	0.512	1.00
29_Q	37_A	0.512	1.00
86_E	91_P	0.510	1.00
15_V	64_E	0.510	1.00
93_G	119_Y	0.508	1.00
74_L	77_M	0.508	1.00
82_S	85_M	0.508	1.00
119_Y	122_V	0.507	1.00
231_L	250_R	0.506	1.00
18_G	57_L	0.506	1.00
100_A	103_V	0.506	1.00
93_G	121_E	0.502	1.00
202_W	205_A	0.502	1.00
69_R	84_I	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
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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
3fzvA	4	0.9408	100	0.097	Contact Map
2esnA	3	0.9605	100	0.1	Contact Map
3hhgA	3	0.9737	100	0.108	Contact Map
1uthA	2	0.7368	100	0.108	Contact Map
3fxqA	3	0.9539	100	0.111	Contact Map
1ixcA	4	0.9507	100	0.114	Contact Map
3szpA	3	0.9539	100	0.115	Contact Map
1al3A	1	0.7072	100	0.118	Contact Map
2h98A	2	0.6875	100	0.123	Contact Map
4x6gA	4	0.9868	100	0.125	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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