YFHR - ECOLI - GREMLIN Contacts

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YFHR - Uncharacterized protein YfhR

UniProt:	P77538	Sequences: MALPVNKRVPKILFILFVVAFCVYLVPRVAINFFYYPDDKIYGPDPWSAESVEFTAKDGTRLQGWFIPSSTGPADNAIATIIHAHGNAGNMSAHWPLVSWLPERNFNVFMFDYRGFGKSKGTPSQAGLLDDTQSAINVVRHRSDVNPQRLVLFGQSIGGANILDVIGRGDREGIRAVILDSTFASYATIANQMIPGSGYLLDESYSGENYIASVSPIPLLLIHGKADHVIPWQHSEKLYSLAKEPKRLILIPDGEHIDAFSDRHGDVYREQMVDFILSALNPQN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13453
Length:	284 (222)
Sequences:	25437 (18500)
Seq/√Len:	1241.6

ECOLI - YFHR FRSA PLDB YCJY YJFP DLHH RUTD YGHX MHPC YBFF PTRB BIOH MENH
BACSU - YQKD CAH YTMA YBFK YTAP YITV YBDG YUXL NAP RSBQ YUGF YFHM YDJP YQJL YBAC YISY YCGS EST PLBAC MENH YVAM YRAK YCLE
HALSA - Q9HPY2 Q9HN07 Q9HS46 Q9HHP4 Q9HPT9 Q9HP29 Q9HRJ0
SULSO - PIP Q7LX61 Q97WG0 Q97VD6 Q97YB2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
151_V	176_A	4.050	1.00
114_R	131_D	3.434	1.00
166_I	177_V	2.980	1.00
53_E	61_R	2.664	1.00
225_K	252_P	2.627	1.00
239_Y	246_K	2.493	1.00
104_R	273_V	2.460	1.00
249_I	271_Q	2.426	1.00
66_F	107_N	2.358	1.00
232_W	250_L	2.323	1.00
55_T	61_R	2.307	1.00
251_I	271_Q	2.296	1.00
69_S	107_N	2.178	1.00
179_L	182_T	2.156	1.00
57_K	134_S	2.095	1.00
247_R	271_Q	2.040	1.00
225_K	250_L	2.034	1.00
138_V	142_R	1.962	1.00
80_T	107_N	1.961	1.00
162_I	177_V	1.949	1.00
52_V	64_G	1.881	1.00
151_V	276_I	1.831	1.00
84_A	132_T	1.808	1.00
125_Q	128_L	1.795	1.00
214_V	217_I	1.747	1.00
133_Q	165_V	1.742	1.00
236_E	250_L	1.727	1.00
152_L	162_I	1.708	1.00
247_R	278_S	1.684	1.00
133_Q	137_N	1.625	1.00
68_P	107_N	1.596	1.00
67_I	110_M	1.579	1.00
61_R	120_K	1.578	1.00
219_L	242_A	1.555	1.00
163_L	179_L	1.553	1.00
220_L	275_F	1.530	1.00
210_Y	213_S	1.517	1.00
137_N	173_G	1.509	1.00
232_W	236_E	1.501	1.00
85_H	116_F	1.495	1.00
133_Q	169_G	1.494	1.00
109_F	135_A	1.461	1.00
136_I	150_L	1.454	1.00
149_R	175_R	1.434	1.00
223_H	232_W	1.428	1.00
65_W	91_M	1.426	1.00
271_Q	274_D	1.420	1.00
78_I	107_N	1.410	1.00
104_R	277_L	1.409	1.00
164_D	168_R	1.400	1.00
236_E	240_S	1.385	1.00
66_F	109_F	1.384	1.00
50_E	68_P	1.380	1.00
267_V	271_Q	1.377	1.00
63_Q	118_K	1.372	1.00
153_F	180_D	1.370	1.00
159_G	182_T	1.361	1.00
270_E	274_D	1.359	1.00
100_W	104_R	1.358	1.00
140_R	173_G	1.354	1.00
124_S	128_L	1.347	1.00
132_T	165_V	1.341	1.00
133_Q	168_R	1.331	1.00
225_K	253_D	1.318	1.00
178_I	272_M	1.313	1.00
84_A	113_Y	1.307	1.00
251_I	254_G	1.306	1.00
84_A	162_I	1.294	1.00
80_T	145_V	1.289	1.00
51_S	63_Q	1.289	1.00
239_Y	248_L	1.281	1.00
146_N	149_R	1.279	1.00
86_G	156_S	1.278	1.00
178_I	276_I	1.265	1.00
81_I	106_F	1.265	1.00
225_K	232_W	1.247	1.00
85_H	113_Y	1.245	1.00
212_A	241_L	1.241	1.00
98_V	110_M	1.235	1.00
138_V	141_H	1.232	1.00
83_H	153_F	1.230	1.00
134_S	137_N	1.229	1.00
106_F	277_L	1.227	1.00
181_S	227_D	1.216	1.00
111_F	135_A	1.213	1.00
223_H	235_S	1.212	1.00
220_L	249_I	1.210	1.00
54_F	135_A	1.209	1.00
155_Q	181_S	1.207	1.00
169_G	173_G	1.200	1.00
273_V	277_L	1.200	1.00
79_A	149_R	1.199	1.00
99_S	103_E	1.187	1.00
236_E	248_L	1.187	1.00
180_D	268_Y	1.178	1.00
251_I	267_V	1.171	1.00
84_A	111_F	1.171	1.00
80_T	109_F	1.144	1.00
109_F	139_V	1.143	1.00
60_T	120_K	1.128	1.00
53_E	63_Q	1.126	1.00
137_N	169_G	1.113	1.00
52_V	138_V	1.104	1.00
151_V	178_I	1.101	1.00
100_W	269_R	1.092	1.00
54_F	64_G	1.092	1.00
79_A	106_F	1.087	1.00
237_K	241_L	1.087	1.00
124_S	127_G	1.084	1.00
151_V	175_R	1.083	1.00
130_D	168_R	1.076	1.00
87_N	157_I	1.071	1.00
226_A	253_D	1.070	1.00
193_M	197_S	1.061	1.00
80_T	139_V	1.054	1.00
97_L	269_R	1.035	1.00
63_Q	112_D	1.035	1.00
177_V	219_L	1.034	1.00
123_P	128_L	1.026	1.00
178_I	220_L	1.023	1.00
100_W	273_V	1.020	1.00
101_L	153_F	1.006	1.00
100_W	103_E	1.005	1.00
91_M	118_K	0.991	1.00
179_L	221_L	0.989	1.00
169_G	172_E	0.987	1.00
136_I	174_I	0.984	1.00
235_S	248_L	0.980	1.00
98_V	102_P	0.973	1.00
165_V	169_G	0.971	1.00
60_T	114_R	0.967	1.00
268_Y	272_M	0.966	1.00
91_M	110_M	0.965	1.00
64_G	109_F	0.965	1.00
57_K	130_D	0.965	1.00
88_A	156_S	0.964	1.00
155_Q	180_D	0.960	1.00
177_V	217_I	0.958	1.00
63_Q	119_S	0.949	1.00
166_I	217_I	0.948	1.00
222_I	251_I	0.947	1.00
88_A	157_I	0.946	1.00
167_G	210_Y	0.943	1.00
222_I	268_Y	0.941	1.00
221_L	239_Y	0.941	1.00
164_D	167_G	0.937	1.00
67_I	102_P	0.930	1.00
178_I	222_I	0.929	1.00
222_I	249_I	0.922	1.00
102_P	108_V	0.920	1.00
51_S	118_K	0.920	1.00
267_V	270_E	0.920	1.00
129_L	164_D	0.918	1.00
221_L	238_L	0.913	1.00
127_G	130_D	0.909	1.00
62_L	119_S	0.907	1.00
135_A	139_V	0.899	1.00
249_I	267_V	0.898	1.00
123_P	127_G	0.895	1.00
64_G	135_A	0.893	1.00
164_D	210_Y	0.892	1.00
266_D	270_E	0.886	1.00
56_A	60_T	0.884	1.00
81_I	108_V	0.883	1.00
58_D	114_R	0.879	1.00
133_Q	173_G	0.878	1.00
84_A	152_L	0.876	1.00
163_L	182_T	0.874	1.00
206_S	209_N	0.867	1.00
243_K	246_K	0.861	1.00
63_Q	91_M	0.851	1.00
237_K	240_S	0.850	1.00
112_D	117_G	0.848	1.00
201_L	204_S	0.846	1.00
113_Y	157_I	0.844	1.00
81_I	153_F	0.838	1.00
168_R	210_Y	0.826	1.00
68_P	102_P	0.826	1.00
254_G	258_D	0.825	1.00
181_S	258_D	0.820	1.00
136_I	165_V	0.819	1.00
94_H	97_L	0.818	1.00
83_H	108_V	0.815	1.00
152_L	165_V	0.814	1.00
137_N	140_R	0.808	1.00
233_Q	236_E	0.807	1.00
126_A	130_D	0.805	1.00
242_A	246_K	0.803	1.00
95_W	99_S	0.803	1.00
203_E	207_G	0.796	1.00
111_F	132_T	0.795	1.00
137_N	141_H	0.794	1.00
254_G	262_D	0.792	1.00
152_L	174_I	0.781	1.00
274_D	278_S	0.780	1.00
80_T	150_L	0.780	1.00
113_Y	161_N	0.778	1.00
106_F	151_V	0.778	1.00
221_L	235_S	0.776	1.00
235_S	239_Y	0.773	1.00
67_I	98_V	0.773	1.00
69_S	78_I	0.772	1.00
83_H	98_V	0.769	1.00
160_A	183_F	0.765	1.00
181_S	257_I	0.758	1.00
203_E	209_N	0.757	1.00
159_G	179_L	0.756	1.00
113_Y	116_F	0.752	1.00
82_I	136_I	0.749	1.00
81_I	101_L	0.736	1.00
181_S	224_G	0.736	1.00
156_S	256_H	0.730	1.00
180_D	222_I	0.728	1.00
247_R	274_D	0.725	1.00
82_I	109_F	0.722	1.00
79_A	151_V	0.717	1.00
176_A	276_I	0.709	1.00
49_A	67_I	0.708	1.00
181_S	223_H	0.698	1.00
228_H	255_E	0.697	1.00
56_A	59_G	0.692	1.00
153_F	272_M	0.682	1.00
239_Y	243_K	0.682	1.00
87_N	116_F	0.681	1.00
51_S	65_W	0.681	1.00
223_H	250_L	0.680	1.00
274_D	277_L	0.680	1.00
56_A	114_R	0.678	1.00
150_L	174_I	0.675	1.00
188_T	234_H	0.675	1.00
106_F	276_I	0.667	1.00
236_E	239_Y	0.665	1.00
132_T	161_N	0.664	1.00
55_T	59_G	0.664	1.00
155_Q	257_I	0.657	1.00
105_N	273_V	0.655	1.00
176_A	218_P	0.654	1.00
75_D	78_I	0.651	1.00
54_F	134_S	0.648	1.00
56_A	134_S	0.647	1.00
83_H	110_M	0.644	1.00
69_S	102_P	0.644	1.00
221_L	242_A	0.643	1.00
140_R	147_P	0.643	1.00
83_H	94_H	0.641	1.00
93_A	96_P	0.640	1.00
154_G	162_I	0.639	1.00
159_G	230_I	0.628	1.00
165_V	174_I	0.628	1.00
91_M	112_D	0.619	1.00
88_A	116_F	0.615	1.00
153_F	178_I	0.613	1.00
148_Q	175_R	0.613	1.00
159_G	183_F	0.613	1.00
183_F	230_I	0.610	1.00
81_I	151_V	0.610	1.00
162_I	166_I	0.609	1.00
130_D	133_Q	0.609	1.00
232_W	248_L	0.608	1.00
112_D	119_S	0.607	1.00
166_I	214_V	0.607	1.00
154_G	166_I	0.604	1.00
129_L	133_Q	0.602	1.00
258_D	261_S	0.602	1.00
223_H	248_L	0.601	1.00
234_H	237_K	0.599	1.00
100_W	266_D	0.597	1.00
50_E	142_R	0.597	1.00
176_A	275_F	0.597	1.00
96_P	99_S	0.595	1.00
172_E	215_S	0.595	1.00
135_A	138_V	0.595	1.00
157_I	161_N	0.592	1.00
67_I	108_V	0.591	1.00
80_T	106_F	0.589	1.00
202_D	205_Y	0.589	1.00
49_A	65_W	0.587	1.00
188_T	237_K	0.584	1.00
93_A	97_L	0.578	1.00
209_N	212_A	0.577	1.00
101_L	108_V	0.576	1.00
220_L	247_R	0.576	1.00
127_G	131_D	0.575	1.00
163_L	238_L	0.571	1.00
256_H	259_A	0.571	1.00
269_R	272_M	0.569	1.00
99_S	102_P	0.569	1.00
154_G	159_G	0.567	1.00
185_S	188_T	0.565	1.00
223_H	230_I	0.563	1.00
160_A	163_L	0.560	1.00
221_L	248_L	0.560	1.00
233_Q	237_K	0.559	1.00
101_L	272_M	0.559	1.00
71_T	78_I	0.559	1.00
130_D	134_S	0.558	1.00
180_D	259_A	0.558	1.00
182_T	223_H	0.557	1.00
66_F	69_S	0.553	1.00
180_D	258_D	0.553	1.00
50_E	66_F	0.552	1.00
185_S	206_S	0.550	1.00
107_N	145_V	0.549	1.00
245_P	278_S	0.545	1.00
211_I	214_V	0.543	1.00
241_L	244_E	0.542	1.00
65_W	92_S	0.542	1.00
126_A	129_L	0.540	1.00
133_Q	136_I	0.540	1.00
211_I	238_L	0.539	1.00
140_R	145_V	0.538	1.00
167_G	214_V	0.534	1.00
180_D	272_M	0.533	1.00
142_R	145_V	0.533	1.00
145_V	148_Q	0.533	1.00
184_A	238_L	0.532	1.00
255_E	258_D	0.530	1.00
100_W	270_E	0.527	1.00
136_I	141_H	0.523	1.00
79_A	148_Q	0.523	1.00
89_G	93_A	0.521	1.00
82_I	111_F	0.520	1.00
65_W	110_M	0.520	1.00
136_I	173_G	0.519	1.00
156_S	257_I	0.519	1.00
123_P	126_A	0.517	1.00
167_G	213_S	0.516	1.00
203_E	206_S	0.513	1.00
64_G	138_V	0.505	1.00
56_A	62_L	0.504	1.00
182_T	230_I	0.503	1.00
126_A	168_R	0.502	1.00
98_V	108_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
4ns4A	1	0.7923	100	0.378	Contact Map
3pe6A	1	0.8239	100	0.383	Contact Map
2wtmA	2	0.7852	100	0.384	Contact Map
2hdwA	2	0.8486	100	0.386	Contact Map
1k8qA	1	0.8838	100	0.39	Contact Map
2y6uA	2	0.8732	100	0.391	Contact Map
1zoiA	3	0.7394	100	0.4	Contact Map
4q1vA	2	0.9683	100	0.404	Contact Map
1mtzA	1	0.757	100	0.407	Contact Map
2ecfA	2	0.9789	100	0.409	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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